crb-blast-0.6.4/0000755000175000017500000000000012577436147013326 5ustar mcrusoemcrusoecrb-blast-0.6.4/metadata.yml0000644000175000017500000001366512577436147015644 0ustar mcrusoemcrusoe--- !ruby/object:Gem::Specification name: crb-blast version: !ruby/object:Gem::Version version: 0.6.4 platform: ruby authors: - Chris Boursnell - Richard Smith-Unna autorequire: bindir: bin cert_chain: [] date: 2015-05-19 00:00:00.000000000 Z dependencies: - !ruby/object:Gem::Dependency name: trollop requirement: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '2.0' type: :runtime prerelease: false version_requirements: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '2.0' - !ruby/object:Gem::Dependency name: bio requirement: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '1.4' - - ">=" - !ruby/object:Gem::Version version: 1.4.3 type: :runtime prerelease: false version_requirements: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '1.4' - - ">=" - !ruby/object:Gem::Version version: 1.4.3 - !ruby/object:Gem::Dependency name: fixwhich requirement: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '1.0' - - ">=" - !ruby/object:Gem::Version version: 1.0.2 type: :runtime prerelease: false version_requirements: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '1.0' - - ">=" - !ruby/object:Gem::Version version: 1.0.2 - !ruby/object:Gem::Dependency name: threach requirement: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '0.2' - - ">=" - !ruby/object:Gem::Version version: 0.2.0 type: :runtime prerelease: false version_requirements: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '0.2' - - ">=" - !ruby/object:Gem::Version version: 0.2.0 - !ruby/object:Gem::Dependency name: bindeps requirement: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '1.0' - - ">=" - !ruby/object:Gem::Version version: 1.0.3 type: :runtime prerelease: false version_requirements: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '1.0' - - ">=" - !ruby/object:Gem::Version version: 1.0.3 - !ruby/object:Gem::Dependency name: rake requirement: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '10.3' - - ">=" - !ruby/object:Gem::Version version: 10.3.2 type: :development prerelease: false version_requirements: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '10.3' - - ">=" - !ruby/object:Gem::Version version: 10.3.2 - !ruby/object:Gem::Dependency name: turn requirement: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '0.9' - - ">=" - !ruby/object:Gem::Version version: 0.9.7 type: :development prerelease: false version_requirements: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '0.9' - - ">=" - !ruby/object:Gem::Version version: 0.9.7 - !ruby/object:Gem::Dependency name: simplecov requirement: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '0.8' - - ">=" - !ruby/object:Gem::Version version: 0.8.2 type: :development prerelease: false version_requirements: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '0.8' - - ">=" - !ruby/object:Gem::Version version: 0.8.2 - !ruby/object:Gem::Dependency name: shoulda-context requirement: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '1.2' - - ">=" - !ruby/object:Gem::Version version: 1.2.1 type: :development prerelease: false version_requirements: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '1.2' - - ">=" - !ruby/object:Gem::Version version: 1.2.1 - !ruby/object:Gem::Dependency name: coveralls requirement: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '0.7' type: :development prerelease: false version_requirements: !ruby/object:Gem::Requirement requirements: - - "~>" - !ruby/object:Gem::Version version: '0.7' description: See summary email: cmb211@cam.ac.uk executables: - crb-blast extensions: [] extra_rdoc_files: [] files: - ".gitignore" - Gemfile - README.md - Rakefile - bin/crb-blast - build - crb-blast.gemspec - deps/deps.yaml - lib/crb-blast.rb - lib/crb-blast/cmd.rb - lib/crb-blast/crb-blast.rb - lib/crb-blast/hit.rb - lib/crb-blast/version.rb - test/helper.rb - test/query.fasta - test/query2.fasta - test/target.fasta - test/target2.fasta - test/test_bin.rb - test/test_test.rb - test/test_test2.rb homepage: https://github.com/cboursnell/crb-blast licenses: - MIT metadata: {} post_install_message: rdoc_options: [] require_paths: - lib required_ruby_version: !ruby/object:Gem::Requirement requirements: - - ">=" - !ruby/object:Gem::Version version: '0' required_rubygems_version: !ruby/object:Gem::Requirement requirements: - - ">=" - !ruby/object:Gem::Version version: '0' requirements: [] rubyforge_project: rubygems_version: 2.2.2 signing_key: specification_version: 4 summary: Run conditional reciprocal best blast test_files: [] crb-blast-0.6.4/test/0000755000175000017500000000000012577436147014305 5ustar mcrusoemcrusoecrb-blast-0.6.4/test/test_test2.rb0000644000175000017500000000440112577436147016731 0ustar mcrusoemcrusoe#!/usr/bin/env ruby require 'helper' class Test2CRBBlast < Test::Unit::TestCase context 'crb-blast' do setup do @blaster = CRB_Blast::CRB_Blast.new('test/query2.fasta', 'test/target2.fasta') @dbs = @blaster.makedb @run = @blaster.run_blast(1e-5, 6, false) @load = @blaster.load_outputs @recips = @blaster.find_reciprocals @secondaries = @blaster.find_secondaries end teardown do extensions = ["blast", "nsq", "nin", "nhr", "psq", "pin", "phr"] Dir["*"].each do |file| extensions.each do |extension| if file =~ /.*\.#{extension}$/ File.delete(file) end end end end should 'setup2 should run ok' do ans = @blaster != nil assert_equal ans, true end should 'break input file into pieces' do files = @blaster.split_input('test/query2.fasta', 4) assert_equal 4, files.size files.each do |file| assert File.exist?(file) end # little teardown files.each do |file| File.delete(file) end end should 'break input file into no more pieces than there are sequences' do files = @blaster.split_input('test/query.fasta', 16) assert_equal 11, files.size files.each do |file| assert File.exist?(file) end # little teardown files.each do |file| File.delete(file) end end should 'run blast should check if the databases exist yet' do tmp = CRB_Blast::CRB_Blast.new('test/query2.fasta', 'test/target2.fasta') assert_equal false, tmp.run_blast(10,1,false) end should 'load output should check if the databases exist' do tmp = CRB_Blast::CRB_Blast.new('test/query2.fasta', 'test/target2.fasta') assert_raise RuntimeError do tmp.load_outputs end end should 'find reciprocals' do assert_equal 7, @recips end should 'add secondary hits' do assert_equal 2, @secondaries end should 'get non reciprocal hits' do count=0 @blaster.missed.each_pair do |key, value| value.each do |i| count+=1 end end assert_equal count,70 end end end crb-blast-0.6.4/test/test_test.rb0000644000175000017500000000510112577436147016645 0ustar mcrusoemcrusoe#!/usr/bin/env ruby require 'helper' class TestCRBBlast < Test::Unit::TestCase context 'crb-blast' do setup do query = File.join(File.dirname(__FILE__), 'query.fasta') target = File.join(File.dirname(__FILE__), 'target.fasta') @blaster = CRB_Blast::CRB_Blast.new(query, target) @dbs = @blaster.makedb @run = @blaster.run_blast(1e-5, 6, false) @load = @blaster.load_outputs @recips = @blaster.find_reciprocals @secondaries = @blaster.find_secondaries end teardown do extensions = ["blast", "nsq", "nin", "nhr", "psq", "pin", "phr"] Dir["*"].each do |file| extensions.each do |extension| if file =~ /.*\.#{extension}$/ File.delete(file) end end end end should 'raise error when files don\'t exist' do query = File.join(File.dirname(__FILE__), 'not_query.fasta') target = File.join(File.dirname(__FILE__), 'not_target.fasta') assert_raise IOError do blaster = CRB_Blast::CRB_Blast.new(query, target) end end should 'setup should run ok' do ans = @blaster != nil assert_equal ans, true end should 'determine that the target is a protein sequence' do prot = @blaster.target_is_prot assert_equal @dbs, ['query', 'target'] assert_equal prot, true end should 'run blast' do assert_equal @run, true end should 'load outputs' do assert_equal @load, [15,15] end should 'find reciprocals' do assert_equal @recips, 10 end should 'check if contig has reciprocal hit' do assert_equal @blaster.has_reciprocal?("scaffold3"), true end should 'not find fake scaffold name' do assert_equal @blaster.has_reciprocal?("not_a_scaffold"), false end should 'get query results' do count=0 @blaster.query_results.each_pair do |key, list| list.each do |hit| count+=1 end end cmd = "wc -l query_into_target.1.blast" lines = `#{cmd}`.to_i assert_equal count, lines end should 'output all reciprocal hits' do a = @blaster.reciprocals assert_equal a["scaffold3"][0].target, "AT3G44735.1" assert_equal a["scaffold5"][0].target, "AT5G13650.2" end should 'run' do blaster = CRB_Blast::CRB_Blast.new('test/query.fasta', 'test/target.fasta') blaster.run 1, 1, false assert blaster.reciprocals end should 'get number of reciprocals' do assert_equal 11, @blaster.size end end end crb-blast-0.6.4/test/test_bin.rb0000644000175000017500000000044412577436147016443 0ustar mcrusoemcrusoe#!/usr/bin/env ruby require 'helper' class TestBinary < Test::Unit::TestCase context 'crb-blast' do should 'run binary' do cmd = "bundle exec bin/crb-blast --help" runner = CRB_Blast::Cmd.new(cmd) runner.run assert runner.status.success? end end end crb-blast-0.6.4/test/target2.fasta0000644000175000017500000005035012577436147016700 0ustar mcrusoemcrusoe>scaffold41641 ATCCCGCGATTCTTAGTACTGCGTAAGTATTTGTACATATATACTGAATACTGATACAAACATGAAAATTTTTGTGTTGACGTATTTTCTTTGAATTTGATGATTATTTCAGGGTTATTTTCGGGATGTTGATAGCGTTACCGATAACTCTAGTCTACTACATCGTTCTTGGATTGTGAAGATCTAAAAAAGAAAAATTTATGAAGTGTCCAAGACAATTGGAATAAGGAATTTTTGACTTGATGCAAGGATCGTGCTACCTCCATCTCCCAA >scaffold41642 ACCCTCCTCCATATCGCCATCGTGCAGGCCGCACTGCCTCAAGGGATTGTTCCTTTTGTTTTTGCAAAAGAGTACAATGTTCATCCCGCGATTCTCAGTACTGCGGTTATTTTTGGGATGTTGATAGCGTTACCGATAACTCTAGTCTACTACATCGTTCTTGGATTGTGAAGATCTAAAAAAGAAAAATTTATGAAGTGTCCAAGACAATTGGAATAAGGAATTTTTGACTTGATGCAAGGATCGTGCTACCTCCATCTCCCAA >scaffold78526 TACATCCCTTTAAGCAAAGGGATTCCCATAACCAATGTGTTTGGTAAAGTTGATAGTGAAAAAAGTGTTATGGACCATTCTATACTGCCCTTTTTGGTGAGGTTGCTCCACGCGGCTAGGACCGCAAGGACAACGAGTTTCTGGAGCGTGTCGGCCGCGATGAACCGAAGGTTCATTTTGTAAGGGTTGTTGGAGGAAATGAAGTGAAAGGAGAGGAGGGGGACGNAAAGAGAGCTACAAATCTGTTGATCCCTGAGCATTGATCAGGGGTGAAGATCTTCCACCATTTCACCGAGCCGTAGGCTAGGATCATGGCGACATAGAGTGGAACGACGGCTGTGAAGACATGGTAAAGGTCCGAAGCCGTGATCATATTGAGAAATTGGA >scaffold87836 GTGGTGGTGGTGGTGGTGGTAAAGATCTTCATATGTTTGTGTGGAGTTCTAGTGCTTCACCTGTATCAGAAGGTGGGATTCATGTGTTTAGAGGTGGGGAGTACGGTAATGATCATGGAGGGGTGCCCCATACTAAAGATTATGATGATTTTGGCCGGAACGAGTTTAGTTTTGGTAATCAACCAGGCCCAAATGGAGTGGACCGTGAAGCGTCGGTTCTATCTAAACTTGGGTCTAGCTCAACTGCAGAGCTCCACCCAAAGGCTAGCCCACATGGTGAAACCAAGCCCCCTTCCATGCCTCCTGCTAGTGTCATGACCAGACTCATTTTGATCATGGTGTGGCGCAAACTTATCAGAAATCCCAACACGTATTCGAGCTTAATTGGCCTCACATGGTCCTTGGTCTCCTTCAAGTGGAACGTTGAAATGCCTGCCATCGTTGCAAAATCCATAGCCATTTTATCCGATGCTGGTCTTGGCATGGCCATGTTTAGCCTCGGTTTGTTCATGGCGTTGCAACCAAAGATTATAGCTTGTGGAAACTCGGTTGCAACCTTTGCCATGGTGGTTCGTTTCTTGATTGGACCGGCGGTCATGGTAGGTGCATCACTGGCTGTTGGACTACATGGAACATTGCTACATGTTGCCATAGTTCAGGCAGCTCTGCCTCAAGGAATTGTCCCTTTTGTGTTTGCTAAAGAATATAATGTCCATCCAGATATACTTAGCACAGGGGTTATATTTGGAATGTTGATAGCACTACCAATTACTCTGGTGTACTACATTGTGTTGGGGCTTTAAATGAGTGGGCTTTGACTCTTGTCTTGTTTGAAGAAGTGAAGTTTAAGTTTGTTTTGGGTTGGGGTTGTCTAACAACATGTGAAATGACCATTTTGTTAATTTTAGTGGAGAGTAAAAAGAGATGACATTAGAGAGGGAGGGTCATTGTTGGGAGGGAGAGAATTGTAATTTGACAAGAAGACATTGGCAGGAAGTAAAGTAAAATCAATGTTTGTTTGTTGTCTCTCCAATTGTTGTTTGTATTGT >C2336898 GCAGGGTACCCTGCACCCCCATGCCCATTCACCTTCACATTACTCCCACTTTCCTCATCATACCCTGCAAAATTCGACCCACGAGGACTCGCACCACTTTTCCCATTAACCATTGAGTAAAAATCAGTGTGATTGAAGCTCGAGCCCCTTGGTGTAGGGTTTCTTGACGACTGTAAAGAGTAAATTTCAGCATTTGTTAAGTTTGATGGCCGAGGGGTTATTGACACACCGGAGTTCATTCCGCCGTGTGACCGCCTTGAGAAGATCTCCGAATGAGAGCTTGCAGACTTCCGAACAGTCACATGAAGCTTCCCATCGTCCCCAACTTCAGCCTCTGTTTGCAATGGCTCTTTACCATCTAACGACAACACATCAGAATCAAC >contig-112109 405 0 AAGTTATCGTTTATGTATTACGGGGACCGTAATGATTGCTGAATAGACTCCATTGCGGTCCCGTGGGGTGGGTACATCTTTTTAATGGAAAAAATCAACATCAATCTCATCAATTAGTTTGTTAAAAGTCGAGGTTCAATTTTTTATTTTGAAAATAAGAGAAATTGATTGAATAATTATAATTTTTCTAGTCAAAACAAGTTTAAAGTTTCAATACTTTGTGGAGACTAATGGCAAATAGAAATAGATTTTGTATCCGATCATAACATGAGTTTCACGAGTTAGGTTATAACTTGGTTGACCTCTGTTTTGTTTTGTTTTTTAATCTTTTGATATATTTATATTTTAAATTTACAATAAATAGTATAAATGTATAGAAAATAAGCACATCTAAATTATAAAATC >contig-233717 356 0 TCCTGATGTTCTGAGCACTGCGGTGATATTTGGAATGATAATATCTTTGCCTATCACAATGCTGTATTACATCTTACTAGGTCTCTAAATGAAGCAAACGGAATTGGGAAACCAGAAAGAAGACTTGATCCATGGATATTCATATGCATATATAATTATACATATCAAGATAAAGGCATACGGTAACTACATATGTCAAACAAAGTTATTTAAGTAAGACTTCAATTTCACATTGATGTTTTGATAAGTTGATAATATGAGTGTTTGAGTAGCACAGTGGTTAGTAGTATTAAGTGTAGTTGTTCTACATTATACTTTCATAATATATATCTCTAGCATAGCTACGTCTTATTCTG >contig-96389 570 0 AGGGAGTTTGATGGTGCAGATTGTGGTGCTTCAGTGCATCATTTGGTACACTTTGATGCTGTTTCTGTTTGAATACAGAGGTGCAAGATTGTTGATTGCTGAACAGTTTCCAGACACTGCTGGTTCGATTATCTCATTTAGGGTTGATTCTGATGTGTTGTCGTTAGATGGTAAAGAGCCATTGCAAACAGAGGCTGAAGTTGGGGACGATGGGAAGCTTCATGTGACTGTTCGGAAGTCTGCAAGTTCTCATTCGGAGATCTTCTCACGGCGGTCACACGGCGGAATGAACTCCGGTGTGTCATTAACCCCTCGTCCATCAAACTTAACAAATGCTGAAATTTACTCTTTACAGTCGTCAAGAAACCCTACACCAAGGGGCTCGAGCTTCAATCACACTGATTTTTACTCAATGGTTAATGGGAAAAGTGGTGCGAGTCCTCGTGGGTCGAATTTTGCAGGGTATGATGAGGAAAGTGGGAGTAATGTGAAGGTGAATGGGCATGGGGGTGCAGGGTACCCTGCTCCGGCGAATGCCGGAATCTTTTCTCCGGTAAGTGGGAAGAGGGG >contig-497662 553 0 CAGAGACCCTTTTCTTCCCAAAACATCTCTCTCATGGACCATCAAACCTTCATTTAAACCCCAATTCCCACCTGGGTTTTCTTCTTCACCATCTTCCTTCACCTGGGTCCTCCTCCAATTTCTCAATATGATCACTGGTTCGGACCTTTACCATGTCTTCACAGCCGTGGTTCCACTCTATGTCGCCATGATCCTAGCCTACGGCTCGGTGAAATGGTGGAAGATCTTCACCCCTGATCAATGCTCAGGGATCAACAGATTTGTAGCTCTCTTTGCTGTCCCATTGCTCTCCTTTCATTTCATCTCAACAAACAACCCTTACACCATGAACACAAGGTTCATCGCCGCTGACACCCTTCAAAAACTCATCGTTCTTGTGGGTCTAGCCTTCTGGTCAAGATTAAGCGCTAGAGGCTCATTAGAATGGTCAATCACTCTGTTTTCTTTATCCACACTTCCCAACACACTTGTGATGGGAATCCCTCTTTTGAAAGGGATGTATGGTGACTTTTCAGGGAGTTTGATGGTGCAGATTGTGGTGCTTCAGTGCATC >contig-428810 267 0 CTGCATTATTGTTGTTCTTTTAATACTAGAGTTTGTTTCTCTCATTGCATCTGTTCCTTCTGCTTCTTGATGGATCTCCTGCTCCTCTTGAATTAAAAGGTGAATTAATGATATCAGCATGATAACAAGATAAAAAGATTAATATATTATAGAACTGAGTGATGCAAGGGTGAATTGTGGCACTGCAATTAATAAAAATATTTGCAGCCCAAGATCTAACTAGCTAGTCTGGATGTTACATGTATAAATGCTGGGAAATGTAATACG >contig-219563 1305 0 CGATATTTATGTTGTTATTTCCATAACTCTCCAAGTACTCTTCTCCGTTACCTTTTACGGGTGATATTGGAACTTTTAAATCTTTTGTAGTTGGTGGGTCGAGTGCTCCGTATTCACGAGCCGCGAATACATCAGAAACCGGGGAAGTGCTCGAGCTCCAAACAAACATGTGTAGATCGTTTGAACCTTCATCTGCTTTTTGCCCGTTAGCCTTTTTGGTTAACGGTATACTTGGTTTTCCAGTTGACGGAGAAAACATCCCAGGATTTGGTGCTGGGTAGTTATTACCACCCAGCACACCATGATGAAAACGAGACTTGTTAGAATTATTCCCACTGCCTTCCTCTTCATAGTTGGAATGACGGGGTGTGGGCCCTCTGGATACAGGAGGCCCATACACATCCGAAGCCCCGAAGTTCGAATTCCTTCCACCAACACCACCCGCCATAGAATAAAAATCATTATGGTTAAAACTCGACCCTCTTGGGGTAGGGTTTCTAGACGATTGCACAGAGTAAATCTCCGCATTCGTCAGATTCGACGGACGAGGGGTCCCAGACGCAAACCCCTGCGACCTCGAGAACACGTCGGATCTCGACGCGTTCGATTTCCGGACCGTCACGTGAATCTTTCCATCCTCTTTAACCTCGGCTTCCGTCTCCAACACTTCCCGTCCATCCAACGACATGATATCCGAATCAACATGAATCGAGGCGATAGCACCTGCGGTCCCCGGGAACTGCTCGGATATCAACAACCTAGCGCCGCGAAACTCGAACAAAAACAACATCAAAGTATACCAAATAATACATTGTAGAACAACAATCTGGACCATTAGGCTACCAGACTCACCACCATACATCCCTTTAAGCAAAGGGATTCCCATAACCAATGTGTTTGGTAAAGTTGATAGTGAAAAAAGTGTTATGGACCATTCTATACTGCCCTTTTTGGTGAGGTTGCTCCACGCGGCTAGGACCGCAAGGACAACGAGTTTCTGGAGCGTGTCGGCCGCGATGAACCGAAGGTTCATTTTGTAAGGGTTGTTGGAGGAAATGAAGTGAAAGGAGAGGAGGGGGACGGCGAAAAGGGCGACAAAGCGGTTGATGCCTGAGCATTGATCAGGGGTGAAGATCTTCCACCATTTGACGGAGCCGTAGGCTAAGATCATGGCGACGTAGAGCGGGACGACCGCGGTCATGACATGGTAGAAGTCTGAAAGAGTGATCATGATGAAGGGGAGAATGAAGTAATTAAGAATGGTGGTTTGAAGGTTTGAAGAGATGAAGAGGGATGTTAAGGAAG >contig-7932 510 0 ATCTTTGGTTGCAACGCCATGAACAAACCGAGGCTAAACATGGCCATGCCAAGACCAGCATCGGATAAAATGGCTATGGATTTTGCAACAATGGCAGGCATTTCAACGTTCCACTTGAAGGAGACCAAGGACCATGTGAGGCCAATTAAGCTCGAATACGTGTTGGGATTTCTGATAAGTTTGCGCCACACCATGATCAAAATGAGTCTGGTCATGACACTAGCAGGAGGCATGGAAGTGGGCTTGGTTTCCCCATGTGGGCTAGCCTTTGGGTGGAGCTCTGCAGTTGAGCTAGACCCGAGTTTGGATAGAACCGATGCTTCACGGTCCACTCCATTCGGGCCTGGTTGGTTCCCAAAACTAAATTCGTTGCGGCCAAAATCATCATAATCTTTAGTATGGGGCACCCCTCCATGATCATTACCGTACTCCCCACCTCTAAACACATGAATCCCACCTTCTGATACAGGTGAAGCACTAGAACTCCACACAAACATATGAAGATCTTTA >contig-245882 614 0 ATCATCACCATACATGGATTTTAAAAGTGGGATTCCCATAACAAGTGTGTTTGGGAGTGTAGAAAGTGAAAACATGGTAATAGCCCAATCCAAGTCTCCTTTTTTCGACAAATTTGTCCATAAAAACAAGACAATTAGTGTCAAAGTCTTTGAAACACCATCGGCTGCTATGAACTTGAGGTTCATTTTGTAAGGATTGATTCTTGAAATGAACTCAAAGGACAACAAAGGGACGGCGAAAATGGCTACAAATCTGTTGATGCCTGCACACTGTTGTGGTGAGAAAATGTTCCATTTTACAGAGGCGTAAGCTACGAACATGGTAATGTAAAGAGGAACAACTGCAGTAAGTACACTATACAAGTCACCAAAGTTGATCATTTCTGCTGGCTTGTTAAGTATTTGGAGGGAAAATGATATGTTTTGAAGCAGTTAAGTGGGAGTTAGTTAAGGCTGTAGAAGCATGGATTTTGATGTCTTGATAGGGCTTAAGAATGCATGGTTTTTTTGTGTGGCACAACTAACCACAGAACACTACACAAGTCACCAAAGCTGATTCCTTATATGGCCTCAATAATGCATTCTTGAGTTGTACGGTACAAGCAATGACGACA >contig-236838 594 0 TGCACTGAAGCACCACAATCTGCACCATCAAACTCCCTGAAAAGTCACCATACATCCCTTTCAAAAGAGGGATTCCCATCACAAGTGTGTTGGGGAGTGTTGACAACGAAAACAGAGTAATCGACCATTCTAACGAGCCTCTGGCGCTCAATCTTGACCAGAAGGCTAGACCCACAAGAACGATGAGTTTTTGAAGGGTGTCAGCAGCGATGAACCTTGAGTTCATGGTGTAAGGATTGTTGGTTGAGATGAAGTGAAAGGAGAGCAATGGGACAGCAAAGAGAGCTACAAATCTGTTGATCCCAGAGCATTGATCAGGGGTGAAGATCTTCCACCATTTCACCGAGCCGTAGGCTAGGATCATGGCGACATAGAGTGGAACGACGGCTGTGAAGACATGGTAAAGGTCCGAAGCCGTGATCATATTGAGAAATTGGAAGATGACCCAGGTGAAAGAAGATGGTGAAGAAGAAAACCCAGGTGGGAATTGGGGGTAAATGAAGGTTATATGAAGGTATGATGAGGGTCCATGAGAGAGAGTAAAATGGTCTCTGGTTTTAAGGGGAAAGGAGGAGCAGAGAGATGTGATGTGTT >contig-430590 396 0 GACAGTATTGATATCGACTTTGTTATGATTGCAGGCATATTAACATTCCATCTGAAACATACTAGAGACCAGACGAGACCGATTAAACTTGAATAAGTATTCGGGTTTCTAATCAGTTTCCTCCACACCATTATCAGTATCAGTCTGGTCATCACGCTCGTTGGTGGCATTGCATTGTTGCCAACAATGCCTGCGCCAGTCCCTTCAATGTTTATGTTGTTATTTCCGTAACCCTCCAAGTACTCTGCTCCGTTACCTTTTACGGGTGATATGGGAACTTTTAAATCTTTTGTAGTTGGCTGGTCGAGTGCTCCGTATTCACGAGCCGCGAATACATCAGAGACCGGGGAATTACTCGAGCTCCAAACAAACATGTGTAGATCATTTGAACCTTCG >contig-58203 379 0 GTTCAAATGATCTACACATGTTTGTTTGGAGCTCGAGTAATTCCCCGGTCTCTGATGTATTCGCGGCTCGTGAATACGGAGCACTCGACCAGCAAACTACAAAAGATTTAAAAGGTAACGGAGAAGAGTACTTGGAGAGTTATGGAAATAACAACATAAACATCGAAGGGGCTGGCGCAGGCATTGTTGGCAACAATGTAATGCCTCCAACGAGTGTGATGACTAGACTGATACTGATAATGGTGTGGAGGAAACTGATTAGAAACCCGAATACTTATTCGAGTTTAATCGGTCTCGTCTGGTCTCTAGTATGTTTCAGATGGAATGTTAATATGCCTGCAATCATAACAAAGTCGATATCAATACTGTCTGATGCAGG >contig-104976 401 0 TTTACTTTACTTCCTGCCAATGTCTTCTTGTCAAATTACAATTCTCTCCCTCCCAACAATGACCCACCCTCTCTAATGTCATCTCTTTTTACTCTCCACTAAAATTAACAAAATGGTCATTTCACATGTTGTTAGACATCCCCAACCCAAAACAAACTTAAACTTCACTTCTTCAAACAAGACAAGAGTCAAAGCCCACTCATTTAAAGCCCCAACACTATGTAGTACACCAGAGTAATTGGTAGAGCTATCAACATTCCAAATATAACCCCTGTGCTAAGTATATCTGGATGGACATTATACTCTTTAGCAAACACAAAAGGGACAATTCCTTGAGGCAGAGCTGCCTGAACTATGGCAACATGTAGCAATGTTCCATGTAGTCCAACAGCCAGTGATGC >contig-498074 549 0 AAAAGATTCCGGCATTCGCCGGAGCAGGGTACCCTGCACCCCCATGACCCCCATTCACCTTCACATTACTCCCACTTTCCTCATCATACCCTGCAAAATTCGACCCACGAGGACTAGCACCACTTTTCCCATTAACCATTGAGTAAAAATCAGTGTGATTGAAGCTCGAGCCCCTTGGTGTTGGGTTTCTTGACGACTGTAAAGAGTAAATTTCAGCATTTGTTAAGTTTGATGGCCGAGGGGTTATTGACACACCGGAGTTCATTCCGCCGTGTGACCGCCTTGAGAAGATCTCCGAATGAGAGCTTGCAGACTTCCGAACAGTCACATGAAGCTTCCCATCGTCCCCAACTTCAGCCTCTGTCTGCAATGGCTCCTTACCATCTAACGACAACACATCAGAATCAACTCTAAAAGAAATAATCGAACCAGCAGTGTCTGGAAACTGCTCAGCGATCAACAATCTTGCACCTCTGTATTCAAACAGAAACAGCATCAAAGTGTACCAAATGATGCACTGAAGCACCACAATCTGCACCATCAAACTCC >contig-474480 309 0 GTTATTTTTGGGATGTTGATAGCGTTACCGATAACTCTAGTCTACTACATCGTTCTTGGATTGTGAAGATCTAAAAAATGAAAATTTTATGAAGTGTCCAAGACAATTGGAATAAGGAATTTTTGACTTGATGTAAGGATCGTGCTACCTCCATCTCCCAATGTTGTATCTTTTAATGTGTAGATTCTCAAGAAATGAGGAAAGCAAGAAAGAAGATATAGTTTAAAAGAGGGGGAGACAAACATGAGCAAAAGAAGGAAATTTAATCTTTTTTTTTCTTCTTTTTTGGGGGAAAAAAAGAAAAATCTT >contig-357246 874 0 GATATTCGAAAACACCACCCTAAAAAAACACTTCATCTTCTTCACATCCTGAAAACCTGCAAATCTCCATTGTCATCTCACCATGATCACTCTTTCAGACTTCTACCACGTCATGACCGCCGTAGTCCCCCTCTACGTCGCCATGATCCTCGCCTACGGCTCCGTCAAATGGTGGAAGATCTTCACCCCCGATCAATGCTCCGGCATCAACCGCTTTGTCGCCCTCTTCGCCGTCCCCCTCCTCTCCTTCCACTTCATCTCCACCAACAATCCCTACACCATGAACCTCAAATTCATCACCGCTGACACCCTCCAGAAGCTCGTTGTCCTCGCTGCCCTTGCCGCCCTCGCCAACCTCACCAAACTCGTTAGCCTCGAGTGGTCGATCACACTCTTTTCACTTTCGACTTTGCCCAATACCCTTGTTATGGGCATCCCTTTGCTTAAAGGGATGTATGGGGGTGACTCTGGGAGTTTAATGGTTCAGATTGTGGTTTTGCAGTGTATTATTTGGTATACTTTGATGTTGTTTTTGTTTGAGTTTCGCGGGGCCCGGATGCTCATCTCTGAGCAGTTTCCGGGCTCCGCGGGCGCGATCGGGTCGATACATGTCGACCCGGACGTCGTGTCGTTGGACGGGCGGCACATGTTGGAGACCGAGGCGGAGGTGAAGGAGGACGGGAAGCTTCGTGTTACGGTGCGGAAGTCGAACGCGTCGAGGTCGGACGTGGTTTCGAGACGGTCACATGGGTTTTCGGGCGTGACGCCTCGTCCGTCGAATCTGACGAATGCGGAGATTTACTCTCTGCAGTCGTCGAGAAACCCGACCCCGAGAGGGTCGAGTTTTAATCATAATGATTTTTATTCGATGGCT >contig-358147 1348 0 GGAAAATACTACAAAATTACCATCCCCACCACCACCTTTGGAGCCTTAAAACACTTAACTCTTAAAACCTTCAAAGCACCAACATTCGCTAGTTCCCCTTGACGTACCATGATCAGTGTTTCAGATTTGTACCATGTGATGACGGCGGTCGTCCCGCTGTACGTGGCGATGATCTTAGCGTACGGGTCGGTCAAATGGTGGAAGATCTTCAGCCCTGATCAATGCTCAGGCATCAACCGGTTTGTCGCCCTTTTCGCCGTCCCCCTCCTCTCCTTTCACTTCATTTCCTCCAACAACCCTTACAAAATGAACCTTCGCTTCATCGCCGCCGACACCCTCCAAAAACTAGTCGTCCTCGCCGTCCTAGCCGCCTGGAGCAACCTTACTAAAAGGGGTAGTTTAGAATGGTCCATAACATTTTTTTCACTTTCAACTTTACCCAACACGTTGGTTATGGGGATCCCTTTGCTTAAAGGGATGTATGGTGGTGAGTCTGGTAGTCTAATGGTCCAAATTGTTGTCCTACAATGCATTATTTGGTATACTTTGATGTTGTTTTTGTTCGAGTTTCGCGGCGCCAGGTTGTTGTTATCCGAGCAGTTCCCTGGGACCGCCGGTGCCATCGCCTCGATTCATGTCGATTCCGATATCATGTCGTTGGATGGACGGCAAGTGTTGGAGACGGAAGCCGAGGTTAAAGAGGACGGAAAGCTTCACGTGACAGTCCGGAAGTCGAATGCGTCCAGATCCGACGTGTTCTCGAGAAGGTCGCAGGGGTTTTCGTCCACGACCCCTCGGCCGTCGAATCTAACGAATGCAGAGATTTACTCTCTGCAGTCGTCTAGAAACCCAACCCCGAGAGGGTCGAGTTTTAACCACAATGATTTTTATTCTATGGCGGGTGGTGTTGGTGGTAGGAATTCCAACTTCGGGGCGTCAGATGTGTATGGGCCTCCTGTATCCAGAGGGCCCACGCCCCGTCATTCCAACTATGAAGAGGAATGCAGTGTGAATAATGCTAACAAGTCTCGTTTCCATCACGGGGGGGTGCTGGGTGGAAATAACTATCCAGCACCAAATCCCGGGATGTTTTCTCCGTCAACAGGAAAACCAAGTATACCGTTAACCAAAAAGGCTAACGGGCAAAAAGCGGACGAAGGTTCAAATGATCTACACATGTTTGTTTGGAGCTCGAGTACTTCCCCGGTTTCTGATGTATTCGCGGCTCGTGAATACGGAGCACTCGACCCGCCAACTACAAAAGATTTAAAAGTTCCAATATCACCCGTAAAAGGTAACGGAGAAGAGTACTTGGAGAGTTATGGAAATAACAACATAAATATCGAAG >contig-492356 636 0 GGTGATATTCGGCATGTTGATTGCGTTACCAATAACTCTAGTCTACTACATTCTTCTTGGTTTGTAAGGTGTATGATTAAGGTATAAAACATGGGAAAGAGGAAGAAATCTTTAAGACAGAATGTCGTTTGTTTGATTTGTTTAAGTCAAAAATTCGGTCATTGGTTTATACGTTAAGCGCGAACTGAATCAACACGAAGATGAAAATTTTGACTTGATTTGAAGCACTCGTCCTTGATCTAAGGTTCTTGCTACCCCTGAAACTACAACCCACAAATTAGATTCTATAGTTTTAAGAAAGCAATCAAGAGATTTATGGCTTTTGAAGAGGGAAACAAGGCAATATGACCATTTGATGGACTACAAGAAGAACAATTTAGTTGTATATTGGTTTGTTAGTGTTGTAACATATATGGTAATATTGTTTGTTTTTCTTTTAACATAATAATTACTTTAAAATTATTATGAGTAAAAGACGTGTATCGTAATATGGTTATTGGAATGTAGTTGTCTTTGTAATATAATGGTAAGATTTATGTTAGGTTGCAAATGAAGGTTTTTTTTGTTGGTTTAAAATCGACATGTGATAGACGATCATGTACCTTGTTTTGAATCGGATTTTAAAAATCACGGGTG >contig-525045 392 0 TACATAAACTACATTAACTACGACGAGTTTAACATTTTGTTGAATAATATTAACTTGACTAAACAATGTGAACCAAATTTCATTTAAGCAACCACCAACCATCCTTTTCTATTTCTAGCAACTAACAACCTGAAAACTACTTAACGAACTACTTTCTAGCATCCGTGTTGACGTATTTTCCGCCAAAGTATGACGATGTCAACCTTGTCTATTTTAACCCCAATAGAATGTAGTAGACAAGCGTGATAGGTAACGCTATTAGCATTCCAAATATAACACCAGTACTGAGGATATCAGGATGAACGCTGTACTCCTTAGCAAAGACAAAGGGGACAATACCCTGTGGTAAAGCAGCCTGGACAATTGCAATGCGTAAAAGGACGCCACGTAGG >_9982 TACTTTTGTTCTGGTCTATCAATTTTCCTGCATAATTTCATCCCACAAACACACACAACAAAAAAAACACACAAAGGCAAAAGATATTAAAAAAACCCCATCCCTTTTTGAGTTTTTGTACACTGCAAAAAACACTTGATGATCTTCTTCTTCTTCTTCTTCACAATCACATACCTTTGAAAACCTGCAAATCTCCATTGTCATCTCACCATGATCACTCTCTCAGATTTCTACCACGTCATGACCGCCGTGGTCCCCCTGTACGTGGCCATGATCCTGGCCTACGCCTCCGTGAAATGGTGGAAGATCTTCTCCCCCGATCAATGCTCCGGCATCAACCGCTTCGTCGCCCTCTTCGCCGTCCCCCTCCTCTCCTTCCACTTCATCTCCACCAACAATCCTTACCAAATGAACCTCAGATTCATCGCCGCTGACACCCTACAGAAGCTGGTGGTTCTCGTCGCCCTCGCCCTCGTCGCCAACCTCACCAAACTCGTTAGCCTCGAGTGGTCCATCACATTCTTTTCGCTTTCGACTCTGCCCAACACCCTTGTCATGGGCATCCCTTTGCTTAAAGGGATGTATGGGGGTGACTCTGGGAGCTTAATGGTTCAGATTGTTGTTTTGCAGTGTATTATTTGGTACACTTTGATGTTGTTTTTGTTTGAGTTCCGCGGGGCCCGCATGCTCATCTCTGAGCAGTTTCCGGGTTCCGCGGGGGCGATCGGGTCGATTCATGTCGACCCGGACGTCGTGTCGCTGGATGGACGACACGTGTTGGAGACGGAGACCGAGGTGAAGGAGGACGGGAAGCTTCGTGTTACGGTGAGGAAGTCGAACGCGTCGAGGTCGGACGTGGTTTCGAGACGGTCGCATGGGTTTTCGGGCGTGACGCCTCGCCCGTCGGATCTGACGAATGCGGAGATTTACTCTCTGCAGTCGTCGAGAAACCCGACCCCGAGAGGGTCGAGTTTTAATCATAATGATTTTTATTCGATGGCTGGGGGTGGTGGTGGCGGAGGGAGGAATTCGAACTTTGGGCCTTCGGATGTGTACGGGCCTCCGGTTTCCAGAGGCCCGACGCCTCGGTCTTCTAACTATGAAGGGGAAGGCGGAGGGAGTACTGCGGGTAATAAAACTCGTTTTCATCATGGGGTGATGGGTGGTAACTACCCAACACCGAATCCTGGGATGTTTTCCCCGTCAACAGGAAAACCGAGTGAACCGTTGAATAAAAAGGTTAACGGGCAAAAAATAGCAGACGAAGGTTCAAATGATCTACACATGTTTGTTTGGAGCTCGAGTAATTCCCCGGTCTCTGATGTATTCGC >_25713 TGTTCTTTTAATACTAGAGTTTGTTTCTCTCATTGCATCTGTTCCTTCTGCTTCTTGATGGATCTCCTGCTCCTCTTGAATTAAAAGGTGAATTAATGATATCAGCATGATAACAAGATAAAAAGATTAATATATTATAGAACTGAGTGATGCAAGGGTGAATTGTGGCACTGCAATTAATAAAAATATTTGCAGCCCAAGATCTAACTAGCTAGTCTGGATGTTACATGTATAAATGCTGGGAAATGTAATACGATAAGAATTTTTGTGCTTATTTATGTTGGAGTTGCTCTTATAAGAGTGCTTAGCATAAAAAATTTGGACGCTTACAAATTGCATGTGTATAGTCTATAGATGAGTTTGTCGCACACAATTTCTCACACTTCATCTCTTGTGAGGCAACGAGGCATAACAAATTGATCTCTACACTGCAAGACATATTTTATGTTCTTGCATGCTTGTAAGTGCAAACATTTTTGTACAGCTTATGTTCAATTTTTTTTATTTTATATATACTAGTGCTTTTAAATGTTAAAATTTTGCATGGTTATAAGCCTGAACAACTAGATACAAATTTACACACATTCTTAAGCCATGTAGAAAAAAAGTGTGCAAATTATATATCTGCTGTACTGTTTCATGGCTACTAAGTTTAAATAAAAAGTTTTATCATAGAAGGTATGATCCCACTGCATCCTCTTGAATATCAACCCCACACATTCTTATTTGATCTGTTGGAGTGCCTTAAATGCAGATGTTTATTGCATTTGTTGCTTGTTATATAACTCCCCTATTACTATTAGGCTATAACTATATGAGGTTTACATTCAAGATTCAACATAAATAAATAAATAAAAACTATAAATACGTACCTGTGGCAGCAAATGACTGTATCATGTGAACTTCCCTTGCAGTTGACAGCTCAAACAGGAATAATAACAAATTATA >_36964 CACACAAAAAAAAACACAAAGACAAAAGATATTCGAAAACACCACCCTAAAAAAACACTTCATCTTCTTCACATCCTGAAAACCTGCAAATCTCCATTGTCATCTCACCATGATCACTCTTTCAGACTTCTACCACGTCATGACCGCCGTAGTCCCCCTCTACGTCGCCATGATCCTCGCCTACGGCTCCGTCAAATGGTGGAAGATCTTCACCCCCGATCAATGCTCCGGCATCAACCGCTTTGTCGCCCTCTTCGCCGTCCCCCTCCTCTCCTTCCACTTCATCTCCACCAACAATCCCTACACCATGAACCTCAAATTCATCACCGCTGACACCCTCCAGAAGCTCGTTGTCCTCGCTGCCCTTGCCGCCCTCGCCAACCTCACCAAACTCGTTAGCCTCGAGTGGTCGATCACACTCTTTTCACTTTCGACTTTGCCCAATACCCTTGTTATGGGCATCCCTTTGCTTAAAGGGATGTATGGGGGTGACTCTGGGAGTTTAATGGTTCAGATTGTGGTTTTGCAGTGTATTATTTGGTATACTTTGATGTTGTTTTTGTTTGAGTTTCGCGGGGCCCGGATGCTCATCTCTGAGCAGTTTCCGGGCTCCGCGGGCGCGATCGGGTCGATACATGTCGACCCGGACGTCGTGTCGTTGGACGGGCGGCACATGTTGGAGACCGAGGCGGAGGTGAAGGAGGACGGGAAGCTTCGTGTTACGGTGCGGAAGTCGAACGCGTCGAGGTCGGACGTGGTTTCGAGACGGTCACATGGGTTTTTCTTGACTTCCACACTACTGTTGACTAAACTACATATA >_87167 AGGTTTGTTCATGGCTTCACAACCAAAGCTTATAGCATGTGGGAAGAGATTAGCAGCATATGGGATGGTAGCAAGGTTTGTAGCAGGACCTGCTGTGATGGCGATTGCTTCTATAGCTGTAGGTCTAAGAGGCACAATCCTACAAGTTTCTATCGTACAAGCGTCTTTACCACAAGGGATTGTGCCATTTGTGTTTGCTCGGGAGTACAACCTCCATCCTGATGTTCTGAGCACTGCGGTGATATTTGGAATGATAATATCTTTGCCTATCACAATGCTGTATTACATCTTACTAGGTCTCTAAATGAAGCAAACGGAATTGGGAAACCAGAAAGAAGACTTGATCCATGGATATTCATATGCATATATAATTATACATATCAAGATAAAGGCATACGGTAACTACATATGTCAAACAAAGTTATTTAAGTAAGACTTCAATTTCACATTGATGTTTTGATAAGTTGATAATATGAGTGTTTGAGTAGCACAGTGGTTAGTAGTATTAAGTGTAGTTGTTCTACATTATACTTTCATAATCTATATCACTAGCAAAG >_90885 TTGTGGTGCTTCAGTGCATCATTTGGTACACTTTGATGCTGTTTCTGTTTGAATACAGAGGTGCAAGATTGTTGATCGCTGAGCAGTTTCCAGACACTGCTGGTTCGATTATTTCTTTTAGAGTTGATTCTGATGTGTTGTCGTTAGATGGTAAGGAGCCATTGCAGACAGAGGCTGAAGTTGGGGACGATGGGAAGCTTCATGTGACTGTTCGGAAGTCTGCAAGCTCTCATTCGGAGATCTTCTCAAGGCGGTCACACGGCGGAATGAACTCCGGTGTGTCAATAACCCCTCGGCCATCAAACTTAACAAATGCTGAAATTTACTCTTTACAGTCGTCAAGAAACCCAACACCAAGGGGCTCGAGCTTCAATCACACTGATTTTTACTCAATGGTTAATGGGAAAAGTGGTGCTAGTCCTCGTGGGTCGAATTTTGCAGGGTATGATGAGGAAAGTGGGAGTAATGTGAAGGTGAATGGGGGTCATGGGGGTGCAGGGTACCCTGCTCCGGCGAATGCCGGAATCTTTTCTCCGGTGGGTGGG >_143664 CCAAAAAAAATAGTGAAAGAAGAAAATTAATCATTAGATTTTATAATTTAGATGTGCTTATTTTCTATACATTTATACTATTTATTGTAAATTTAAAATATAAATATATCAAAAGATTAAAAAACAAAACAAAACAGAGGTCAACCAAGTTATAACCTAACTCGTGAAACTCATGTTATGATCGGATACAAAATCTATTTCTATTTGCCATTAGTCTCCACAAAGTATTGAAACTTTAAACTTGTTTTGACTAGAAAAATTATAATTATTCAATCAATTTCTCTTATTTTCAAAATAAAAAATTGAACCTCGACTTTTAACAAACTAATTGATGAGATTGATGTTGATTTTTTCCATTAAAAAGATGTACCCACCCCACGGGACCGCAATGGAGTCTATTCAGCAATCATTACGGTCCCCGTAA >_159544 TCCATCCAGATATACTTAGCACAGGGTGAGTTTTTAATGACTTATACATATCTTATGTCCGTGCATTAATGACTTGTACATATCTTACTTTCGTGCTTTTGTAACTTGCACATCATGCATATGAAAGTTGTACATTGTCAATGTAACAAGTAAATGTGGCATCCAATGGTCATGTTTGAAGAGCAGAGATCCATTGCAACTTTCCCATATCTACTTGTATCCTATGCAATTAAAGTTGTACAATGCTCCAAACATGCAATACTTGTCAAAGAGTACAAGTAGTATCTTGATTTGAAAATGTACAATCTTTAAAGCATGCTTTACTTGTTTGTGTTGCAGGGTTATATTTGGAATGTTGATAGCACTACCAATTACTCTGGTGTACTACATTGTGTTGG >_199159 GTAATTGGTAGAGCTATCAACATTCCAAATATAACCCCGCAAAACAAACATGTAAACCATGTATTAAAGATTTGTACATTTTCAAATCAAGATACTACTACTTATACTCTTTGACAAACATTGCATGTTCGGAGCAATGTACAACTTTTGATGCATAAGATACAAGTAGACATGGCAAAGTTGCAATGGATCTATGCTCTTCAAACATGACCATTAGATGCCACATTAATTTGTTACATTTGACAATGTGCAACTTTCATATGCATTATGTGCAAGTTACTAATGCAGGGAAACAAAATATGTACAAATCGTTAATGCACAAAAGTATTTAAAACTCACCCTGTGC >_199413 AAAAAAACACACACACACACACACAAAGGGGAAAATACTACAAAATTACCATCCCCACCACCACCTTTGGAGCCTTAAAACACTTAACTCTTAAAACCTTCAAAGCACCAACATTCGCTAGTTCCCCTTGACGTACCATGATCAGTGTTTCAGATTTGTACCATGTGATGACGGCGGTCGTCCCGCTGTACGTGGCGATGATCTTAGCGTACGGGTCGGTCAAATGGTGGAAGATCTTCAGCCCTGATCAATGCTCAGGCATCAACCGGTTTGTCGCCCTTTTCGCCGTCCCCCTCCTCTCCTTTCACTTCATTTCCTCCAACAACCCTTACAAAATGAACCTTC >_203694 GAAGGTTCATTTTGTAAGGGTTGTTGGAGGAAATGAAGTGAAAGGAGAGGAGGGGGACGGCGAAAAGGGCGACAAAGCGGTTGATGCCTGAGCATTGATCAGGGGTGAAGATCTTCCACCATTTGACGGAGCCGTAGGCTAAGATCATGGCGACGTAGAGCGGGACGACCGCGGTCATGACATGGTAGAAGTCTGAAAGAGTGATCATGATGAAGGGGAGAATGAAGTAATTAAGAATGGTGGTTTGAAGGTTTGAAGAGATGAAGAGGGATGTTAAGGAAGTGAAGTGTTTTGAGGCTCCAAAGGTGGTGGGGGCTTGTTTTGTAGTATTTTCCACTTTG >_278972 CTCTGCTCCTCCTTTCCCCTTAAAACCAGAGACCCTTTTCTTCCCAAAACATCTCTCTCATGGACCATCAAACCTTCATTTAAACCCCAATTCCCACCTGGGTTTTCTTCTTCACCATCTTCCTTCACCTGGGTCCTCCTCCAATTTCTCAATATGATCACTGGTTCGGACCTTTACCATGTCTTCACAGCCGTGGTTCCACTCTATGTCGCCATGATCCTAGCCTACGGCTCGGTGAAATGGTGGAAGATCTTCACCCCTGATCAATGCT >_288182 CGAGTATAATGTTCACCCAGAAATCCTGAGCACCAGCTAACTAGAAGAGGATTCGTTCAAGCAAATGATAAAAAGCTAGAAGGCACCAAGATATTTCAAGCCCAGGAATTAGAACACATCAGCATGATATCTCGTCATTCGTTGTAGTGAAGGGTTAAAGATCAGTACAAGATTACATAAATCTTGTAAAGTTCATGTCCAAAAAACCACCATTCTACGAGTCTGTTGTTGTATTAACTTGTCTATTTATGAACCTAGTTTACA >_307804 CCCTCTTCCCTTTATATACAACTTCCCCACCCCCCCCCCACTTTCTAATTTCTCTCGCCGGAACTTCCATCTCCGTCAACGGTAAAACCGCCACAAATCACCCACATTCCGGTTACAAAACCGTCACAAAAGATAACAAACTCCCACTCTCACTCTCACTTTCCCATTTTACCCCCACCACCACCACAATGATCACCGCCCACGACTTCTACACCGTCATGTCCGCCATGGTGCCGTTATACGTCGCCAT >_350457 GAAACCACAGATTCTTGAAAATTCAGTTACCATTCTCTCAGATGCAGGCCTAGGAATGGCTATGTTTAGTCTAGGTAAATATGAAAATAGAGAAGGCATTTTTGAATAAACGGGTCTATTTGGGTTGTGTTTTATCTAATACAGTCTAAATGGCTCAAATCAAAATATGCAACTGTAAAGGGAACGGGTCAAATGAGTCGAAAATGGCGCAAAAATCAATTTTTA >_362402 CGAAGTTTGACAACCTCCCACCCGGAAACCCCATCATGGAGTAAAAAATCCGAGTGGTTAAAATTCGAACCTCGCGGGGTCGGATTCCTCGACGAGCTCAAACTATAAATTTCCGCCCCCGTAAGGTTCGACAGCCGGGGAGTCATCTGACTCCCCGACCCAAACCCTACCGACTTCCTCGACACATTCGACCTCCTCACCGTCACATGTAACTTCCCA crb-blast-0.6.4/test/target.fasta0000644000175000017500000004237612577436147016627 0ustar mcrusoemcrusoe>AT2G39730.1|PACid:19639427 MAAAVSTVGAINRAPLSLNGSGSGAVSAPASTFLGKKVVTVSRFAQSNKKSNGSFKVLAVKEDKQTDGDRWRGLAYDTSDDQQDITRGKGMVDSVFQAPMGTGTHHAVLSSYEYVSQGLRQYNLDNMMDGFYIAPAFMDKLVVHITKNFLTLPNIKVPLILGIWGGKGQGKSFQCELVMAKMGINPIMMSAGELESGNAGEPAKLIRQRYREAADLIKKGKMCCLFINDLDAGAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPGMYNKEENARVPIICTGNDFSTLYAPLIRDGRMEKFYWAPTREDRIGVCKGIFRTDKIKDEDIVTLVDQFPGQSIDFFGALRARVYDDEVRKFVESLGVEKIGKRLVNSREGPPVFEQPEMTYEKLMEYGNMLVMEQENVKRVQLAETYLSQAALGDANADAIGRGTFYGKGAQQVNLPVPEGCTDPVAENFDPTARSDDGTCVYNF >AT2G24270.4|PACid:19639899 MAGTGLFAEILDGEVYKYYADGEWKTSSSGKSVAIMNPATRKTQYKVQACTQEEVNAVMELAKSAQKSWAKTPLWKRAELLHKAAAILKDNKAPMAESLVKEIAKPAKDSVTEVVRSGDLISYCAEEGVRILGEGKFLLSDSFPGNDRTKYCLTSKIPLGVVLAIPPFNYPVNLAVSKIAPALIAGNSLVLKPPTQGAVSCLHMVHCFHLAGFPKGLISCITGKGSEIGDFLTMHPAVNCISFTGGDTGISISKKAGMIPLQMELGGKDACIVLDDADLDLVASNIIKGGFSYSGQRCTAVKVVLVMESVADELVEKVKAKVAKLTVGPPEENSDITAVVSESSANFIEGLVMDAKEKGATFCQEYKREGNLIWPLLLDNVRPDMRIAWEEPFGPVVPVLRINSVEEGINHCNASNFGLQGCVFTKDINKAILISDAMETGTVQINSAPARGPDHFPFQGLKDSGIGSQGVTNSINLMTKVKTTVINLPTPSYSMGDGFISRL >AT2G44920.2|PACid:19640483 MVILSNVSLFSCCNISQKPSLFSPSSRSSHCPIRCSQSQEGKEVVTSPLRSVVWSLGEEVSKRSLFALVSASLFFVDPALAFKGGGPYGQGVTRGQDLSGKDFSGQTLIRQDFKTSILRQANFKGAKLLGASFFDADLTGADLSEADLRGADFSLANVTKVNLTNANLEGATVTGNTSFKGSNITGADFTDVPLRDDQRVYLCKVADGVNATTGNATRDTLLCN >AT2G36370.1|PACid:19640825 MSEILSYGSVKVRAHRTRLIQESSYFHGLLSGSFSESGLDHISVEWNLESFLNLLMCLYGYDIEITSSSFLPLFESALYFGVEKLLSICKNWLSVLASSNDNALPKVELSDLIQIWSFGLEHAGEFVPDLCVAYLAKNFMLVKSDKYFGNVPYELLMWCVKHPHLTVHSEMDLVDGLLIWLDAGGRLSDLPESSQDNTINLMEQVRFSLLPLWFIAGRSKSHGFSKFADQSIELVTKLMKMPSTCLVDSLTDGPPTDVRVRLTEYSEILDLSGCPQLNEASLLLSILPNSYFANLRWRKSLESFLKNPDDDERHQEQISHRTLPILSFESVKEIDISKCQRLDYKVVIKCFSKSFPSLRKLRAAYLLNIKVSTLLELLLNFRELTEVDLTVDVSPIIPVQASVFYSGQGHCLLSSITRLTLEGRSDICDMELRSISRVCESLCYLNIKGCALLSDACIASVIQRCKKLCSLIVCYTSFSENSILALCATISMTNEHMDINSVASNLQTLHMSKCEGISETSLLNLITHSQKMKSLCLRDTKVSDSVLCEFPGSTLEALDISNTTISWMALARVISRNPNLKTLKARGCKNLLQLEVDGRTDNFSPLVSGQEVFKCLSKGSGLEELEIGWGFSYFSFESLRPAASFLRVISVGLGASLGEDVLKLLPSTCPLLESIVLHFQEISDSALTSVLTSLKHLQELALSYCFGEISLQSFKFSMPNLRKLRLERVTRWMTNDDLLVLTQSCPNLTELSLVGCLHLTSDCQPIISAGWPGMISLHLEECGSITENGVASLYGCIALEDLFLRHNGSGIQKSFLLDATLKFPMLRLVSLDMCDAKEGGFDVPEEKEEGRSLSIVKISRCKSDRCSLGRRAAPMHRETLVMLWNGQTLTKTLLKQRL >AT2G42520.1|PACid:19641881 MSASWADVADSENTGSGSSNQNSHPSRPAYVPPHLRNRPAASEPVAPLPANDRVGYGGPPSGSRWAPGGSGVGVGGGGGYRADAGRPGSGSGYGGRGGGGWNNRSGGWDRREREVNPFENDDSEPEPAFTEQDNTVINFDAYEDIPIETSGDNVPPPVNTFAEIDLGEALNLNIRRCKYVKPTPVQRHAIPILLEGRDLMACAQTGSGKTAAFCFPIISGIMKDQHVQRPRGSRTVYPLAVILSPTRELASQIHDEAKKFSYQTGVKVVVAYGGTPINQQLRELERGVDILVATPGRLNDLLERARVSMQMIRFLALDEADRMLDMGFEPQIRKIVEQMDMPPRGVRQTLLFSATFPREIQRLAADFLANYIFLAVGRVGSSTDLIVQRVEFVLDSDKRSHLMDLLHAQRENGIQGKQALTLVFVETKRGADSLENWLCINGFPATSIHGDRTQQEREVALKAFKSGRTPILVATDVAARGLDIPHVAHVVNFDLPNDIDDYVHRIGRTGRAGKSGLATAFFNDGNTSLARPLAELMQEANQEVPEWLTRYASRSSFGGGKNRRSGGRFGGRDFRREGSFGSGRGGYGGGGGGYGGGGGYGGGGGYGGGGGYGGGYGGASSGGYGGEPPSAWD >AT2G24860.1|PACid:19642080 MTICMCCDSHLVAKSILNPWNSPRITKLGFVPVVRRFPATTTVKASAVDSPESSSNFAKRMDQAWIISQQPSPVGCSSCNSKGHVECKWCAGTGFFILGDNMLCQVPSRNTSCVICSGQGSASCSDCKGTGFRAKWLEKPPVPT >AT2G47840.1|PACid:19642428 MASLCLSLHQTLTNPLSAPRCRPLSLSFPGSSTFSIRPSSRRATALTTRASYTPTPATERVISIASYALPFFNSLQYGRFLFAQYPRLGLLFEPIFPILNLYRSVPYASFVAFFGLYLGVVRNTSFSRYVRFNAMQAVTLDVLLAVPVLLTRILDPGQGGGFGMKAMMWGHTGVFVFSFMCFVYGVVSSLLGKTPYIPFVADAAGRQL >AT2G26610.1|PACid:19642441 MCSSSDCILPGPPSRSNLSAADLSPSGLLAFASGSSVSLVDSRSLQLISSVSLPSPISCAFSTVTSVRWAPVPVQRDLFSSDLLIAVGDHLGRIALVDFRLCSVRLWLEQSCDSASARGKSLGCGGVQDLCWVLARPDSYVLAAITGPSSLSLYTDSGQLFWKYDASPEYLSCIRCDPFDSRHFCVLGLKGFLLSLKLLGTTENDVPTKEFQIQTDCSDLQKLEREVVASSSHSTCPASAVFPLYSAKFSFSPHWKHILFATFPRELFVFDLKYEAALYVVALPRGYAKFVDVLPDPSQEFLYCLHLDGRLSIWRRKEGEQVHVLCAIEEFMPTIGNSVPSPSLLTLLISQLDSTLQNIRTIHSDALLDSSELEISFDFNNDAFLLFKTHFISISDDGKIWSWILTFNGDEDSNPQTNENLIESPTNGNQDLHPNISFEITLVGQLQLLSSAVTVLAIPTPSMTATLARGGNFPAVVVPLVALGTEAGTIDVVDVSANAVAASFSAHTSSIRGLNWLGNSRLVSYSCSRVSKRTGGYVNKLVVTCLRSGVSRGFRVLQKPERAPIRALRASSSGRYLLILFRDAPVEVWAMTKSPVMLRSLALPFTVLEWTLPTIPSIAQKSLSKQLSMSSNQEVNVTPSDIETPNASDSKAVAADALQDDASESFAFALVNGSLGVFEVYGRRIRDFRPKWPASSFISTDGLITAMAYRLPHVVTGDKLGNIRWWDVVSGNSSSFNTCKEGIKKIKFSPVFSGDISRGRITVLFYDNTFSIYDLDSPDPLAISLMRPQIPGTLILELDWLPLRTSKFDSLVLCVAGTDGSFRLVEVHLDEKMTTQIPPKERFRSVPLCTPMLLPTPHALLGVKPSWFNTSSTCIDKRPHSIPGRTSSSKDLRSFMIDFPPIGDPAVLEMFLKVLEPYRSEGCLLDDEKAKLYSSLVNKGCAARFAFAAAIFGETSEALFWLQLPSAMKHVVNKTASKSAKKQFEETATLSKTSSKGPSSTGFEKNGSMSEGQLRLMAFEQKDLWVCANERIPWHEKLEGEEAIQNRVHELVSVGNLEGAVSLLLSTSPDSSYFYPNALRAVALSSTVSKSLVELAVKVVAANMVRSDRSLSGTHLLCSVGRYQEACSQLQDAGCWTDSATLAATHLNGSDYARVLQRWAGHVVNIEHNLWRGVILYVAVGAFEEALAVFRKAERAETAAIFIMACRETLADSWSIDPKNEDVMVVTESYALYQRKLVHLCMDSPPSFH >AT4G23940.1|PACid:19646003 MASIDNVFSLGTRFSIPENPKRSILKHATTSSFSARTQTRWRAPILRRSFTVLCELKTGSSSSGETNNSPAADDFVTRVLKENPSQVEPRYRVGDKLYNLKEREDLSKGTNAATGAFEFIKRKFDSKKKTETDKSEESVYLSDILREYKGKLYVPEQVFGPELSEEEEFEKNVKDLPKMSLEDFRKAMENDKVKLLTSKEVSGVSYTSGYRGFIVDLKEIPGVKSLQRTKWSMKLEVGEAQALLKEYTGPQYEIERHMTSWVGKVADFPNPVASSISSRVMVELGMVTAVIAAAAVVVGGFLASAVFAVTSFAFVTTVYVVWPIAKPFLKLFVGVFLGVLEKSWDYIVDVLADGGIFSRISDFYTFGGVASSLEMLKPILLVVMTMVLLVRFTLSRRPKNFRKWDLWQGIAFSQSKAEARVDGSTGVKFADVAGIDEAVDELQELVKYLKNPDLFDKMGIKPPHGVLLEGPPGCGKTLVAKAIAGEAGVPFYQMAGSEFVEVLVGVGSARIRDLFKRAKVNKPSVIFIDEIDALATRRQGIFKENSDQLYNAATQERETTLNQLLIELDGFDTGKGVIFLGATNRRDLLDPALLRPGRFDRKIRVRPPNAKGRLDILKIHASKVKMSDSVDLSSYASNLPGWSGAKLAQLVQEAALVAVRKTHNSILQSDMDDAVDRLTVGPTRIGLELGHQGQCRRATTEVGVAITSHLLLRYENAKIERCDRVSIIPRGQTLSQVVFHRLDDESYMFGRLPQLLHRLQVLLGGRAAEEVIYGSDTSKASVDYLSDASWLARKILTIWNLENPMVIHGEPPPWRKRPQFVGPRLDFEGSLYDDYDLVEPPVNFNMDDEVAHRSEELISQMYNKTVSLLRQNQTALLKTVKVLLNQKEISGEAIDFILDHYPPQTPLNSLLQEQNPGSLPFVPEHLRRESGDFVLVNHSTDVNAQV >AT4G30870.1|PACid:19646942 MDDERRVLCPENRGLAAYVLQKKQEYAEKPKGLSENLERTFVKGYRSVCDAKDPINTLKDLSQIKGFGKWMVKLMKGYFDTAVESSEQEDLPDNRAGKKANGKKRYIPQRNSVGYALLITLHRRTTNGKEFMRKQELIDAADANGLSHAPVGPEKGKGKAGLGHSKREWYSGWSCMTTLIQKGLVVKSSNPAKYMLTVEGREVANECILRSGLPDSVDILSVDEMDPTPQAKKTPNQNPTCSFTMREELPYVDPRCRAQSAIPSDILEKFTPFGYSKEQVVAAFREVSDGSGDKDPSTLWLSVMCHLRQAEVYNSCPDSRNSKKDSSGPFKSQIRQVDLEGSRAKKFRSCNDGSTLNPCSSGSSHAVKACSSSLASDGTKGITNIPRLPPLQFGETFEEAYDVILILDDREKFATKGSRSRNIVENICSEFNIKIEVRRLPVGDCIWIARHKYLETEYVLDFIAERKNVDDMRSSIRDNRYRDQKLRLQRSGFKKLIYILEGDPNHSDAAESIKTACFTTEILEGFDVLRTHGLGETLRKYGYLTKSIYQYYKLRVNDNDQSKGAASCPSFDSFVKRCQDLDKMTISDVFAIQLMQVPQVTEEIAIAVLDMYPTLLSLASAYSHLEADVSAQEEMLRNRSNNVICASASKNIFKLVWGE >AT4G35335.1|PACid:19646965 MEYRKIKDEDDHDVASDIESVKGKSHTVASSNIAMATLGVGSSERINWKRKGVVTCALTILTSSQAILIVWSKRAGKYEYSVTTANFLVGTLKCALSLLALTRIWKNEGVTDDNRLSTTFDEVKVFPIPAALYLFKNLLQYYIFAYVDAPGYQILKNLNIISTGVLYRIILKRKLSEIQWAGFILLCCGCTTAQLNSNSDRVLQTSLPGWTMAIVMALLSGFAGVYTEAIIKKRPSRNINVQNFWLYVFGMAFNAVAIVIQDFDAVANKGFFHGYSFITLLMILNHALSGIAVSMVMKYADNIVKVYSTSVAMLLTAVVSVFLFNFHLSLAFFLGSTVVSVSVYLHSAGKLR >AT4G29380.1|PACid:19647069 MGNKIARTTQVSATEYYLHDLPSSYNLVLKEVLGRGRFLKSIQCKHDEGLVVVKVYFKRGDSIDLREYERRLVKIKDVFLSLEHPHVWPFQFWQETDKAAYLVRQYFYSNLHDRLSTRPFLSLVEKKWLAFQLLLAVKQCHEKDICHGDIKCENVLLTSWNWLYLADFASFKPTYIPYDDPSDFSFFFDTRGQRLCYLAPERFYEHGGETQVAQDAPLKPSMDIFAVGCVIAELFLEGQPLFELAQLLAYRRGQHDPSQHLEKIPDPGIRKMILHMIQLEPEARLSAEDYLQNYVGVVFPNYFSPFLHTLYCCWNPLPSDMRVATCQGIFQEILKKMMENKSGDEIGVDSPVTSNPMNASTVQETFANHKLNSSKDLIRNTVNSKDEIFYSISDALKKNRHPFLKKITMDDLGTLMSLYDSRSDTYGTPFLPVEGNMRCEGMVLIASMLCSCIRNIKLPHLRREAILLLRSCSLYIDDDDRLQRVLPYVVALLSDPTAIVRCAAMETLCDILPLVRDFPPSDAKIFPEYIFPMLSMLPEDTEESVRICYASNIAKLALTAYGFLIHSFQLSDVGVLNELNSQQISTTPASETPSHLQKANGNAQLQQLRKTIAEVVQELVMGPKQTPNVRRALLQDIGELCFFFGQRQSNDFLLPILPAFLNDRDEQLRSVFFEKIVYVCFFVGQRSVEEYLLPYIDQALSDQTEAVIVNALECLSTLCKSSFLRKRALLQMIECVYPLLCYPSQWVRRAVVTFIAASSECLGAVDSYAFIAPVIRSYLSRLPASIASEEGLLSCLKPPVTREVVYRIFEKTRNPEFMAKQRKMWYSSSPQSKDWESVDLFDKDAGELNSVECRAEQKQSVEGKKQIKSASKQPEVQGKYAEKDAKLRIPRNPRPNASNTVELRDPVYPEKLQFSGFMAPYVSGANSFIEPENIPLYSFSMDKRAATNPPVASESSLQMNSLGMGSLSVPWMDSMSKSFNLASSVPVPKLISGSFHVGTNPKQFYRVVHEPESRENDQISSAISKFQDLGVSSSSKSASVTSEDASSPADLVGEPSLSRTSVPDSGWKPRGVLVAHLQEHRSAVNDIATSSDHSFFVSASDDSTVKVWDSRKLEKDISFRSRLTYHLEGSRGMCTTMLRNSTQVVVGASDGVIHMFSIDHISRGLGNVVEKYSGIVDIKKKDVKEGALVSLLNYTADSLSGPMVMYSTQNCGIHLWDTRSDLDAWTLKANPEEGYVSSLVTSPCGNWFVSGSSRGVLTLWDLRFRVPVNSWQYPIICPIEKMCLCFLPPSVSVSTTMKPLIYVAAGCNEVSLWNAEGGSCHQVLRVANYENETDVSEFQWKLPSNKVNPKPNHRQNMSSKYRIEELNEPPPRLPGIRSLLPLPGGDLLTGGTDLKIRRWDYSSPERSYCICGPSLKGVGNDDFYELKTNTGVQFVQETKRRPLATKLTAKAVLAAAATDTAGCHRDSVQSLASVKLNQRLLISSSRDGAIKVWK >AT4G12110.1|PACid:19648830 MIPYATVEEASIALGRNLTRLETLWFDYSATKSDYYLYCHNILFLFLVFSLVPLPLVFVELARSASGLFNRYKIQPKVNYSLSDMFKCYKDVMTMFILVVGPLQLVSYPSIQMIEIRSGLPLPTITEMLSQLVVYFLIEDYTNYWVHRFFHSKWGYDKIHRVHHEYTAPIGYAAPYAHWAEVLLLGIPTFMGPAIAPGHMITFWLWIALRQMEAIETHSGYDFPWSPTKYIPFYGGAEYHDYHHYVGGQSQSNFASVFTYCDYIYGTDKGYRFQKKLLEQIKESSKKSNKHNGGIKSD >AT1G30090.1|PACid:19651723 MQRVRVSSQRAVVHKLGDSQMTLSPKFRVAASIQSTLFDRSSELELSLRGEPLIPGLPDDVALNCLLRVPVQSHVSSKSVCKRWHLLFGTKETFFAKRKEFGFKDPWLFVVGFSRCTGKIQWKVLDLRNLTWHEIPAMPCRDKVCPHGFRSVSMPREGTMFVCGGMVSDSDCPLDLVLKYDMVKNHWTVTNKMITARSFFASGVIDGMIYAAGGNAADLYELDCAEVLNPLDGNWRPVSNMVAHMASYDTAVLNGKLLVTEGWLWPFFVSPRGQVYDPRTDQWETMSMGLREGWTGTSVVIYDRLFIVSELERMKMKVYDPVTDSWETINGPELPEQICRPFAVNCYGNRVYVVGRNLHLAVGNIWQSENKFAVRWEVVESPERYADITPSNSQILFA >AT1G01060.1|PACid:19652702 MDTNTSGEELLAKARKPYTITKQRERWTEDEHERFLEALRLYGRAWQRIEEHIGTKTAVQIRSHAQKFFTKLEKEAEVKGIPVCQALDIEIPPPRPKRKPNTPYPRKPGNNGTSSSQVSSAKDAKLVSSASSSQLNQAFLDLEKMPFSEKTSTGKENQDENCSGVSTVNKYPLPTKQVSGDIETSKTSTVDNAVQDVPKKNKDKDGNDGTTVHSMQNYPWHFHADIVNGNIAKCPQNHPSGMVSQDFMFHPMREETHGHANLQATTASATTTASHQAFPACHSQDDYRSFLQISSTFSNLIMSTLLQNPAAHAAATFAASVWPYASVGNSGDSSTPMSSSPPSITAIAAATVAAATAWWASHGLLPVCAPAPITCVPFSTVAVPTPAMTEMDTVENTQPFEKQNTALQDQNLASKSPASSSDDSDETGVTKLNADSKTNDDKIEEVVVTAAVHDSNTAQKKNLVDRSSCGSNTPSGSDAETDALDKMEKDKEDVKETDENQPDVIELNNRKIKMRDNNSNNNATTDSWKEVSEEGRIAFQALFARERLPQSFSPPQVAENVNRKQSDTSMPLAPNFKSQDSCAADQEGVVMIGVGTCKSLKTRQTGFKPYKRCSMEVKESQVGNINNQSDEKVCKRLRLEGEAST >AT1G09690.1|PACid:19652733 MPAGHGVRARTRDLFARPFRKKGYIPLSTYLRTFKVGDYVDVKVNGAIHKGMPHKFYHGRTGRIWNVTKRAVGVEVNKQIGNRIIRKRIHVRVEHVQQSRCAEEFKLRKKKNDELKAAAKANGETISTKRQPKGPKPGFMVEGMTLETVTPIPYDVVNDLKGGY >AT1G35660.1|PACid:19655505 MEQSAAPQPPTMPLPYLPSSVEASRDDLQCIGTMVIVPPKPVGFLCGSIPVLADNSFPASFTSALLPSQETVVTAPRYQMLPMETDLNLPPLLTDFPDNVLPLAAVKSRITGDISKEANVITSNLSKKCEALAVSGLVEYGDEIDVIAPVDILKQIFKIPYSKARVSIAVQRVGQTLVLNPGPDVEEGEKLIRRHNNQPKCTKNVDESLFLNFAMHSVRMEACDIPPTHREHTEKRSSSSALPAGENSHDNAPDDRLDKPAGSSKQSKQDGFICEKKKSKKNKAGVEPVRKNSQISEKIKSSGDSEKHSRGGSNEFLRVLFWQFHNFRMLLGSDLLLFSNEKYVAVSLHLWDVSEKVTPLTWLEAWLDNVMASVPELAICYHENGIVQGYELLKTDDIFILKGISEDGTPAFHPHVVQQNGLAVLRFLQSNCKEDPGAYWLYKSAGEDELQLFDLSIISKNHSSSVHNDSASSPSLIHSGRSDSMFSLGNLLYRVGHRLSLSVVPNDRNKCARFLTQCLNCLDAPDHLVVRAYAHEQFARLILNSDEESDLTFESNGVQREVKITDLEEEALDPVTIADHENETVTFSEDKFTEDHSVSNIVPLVSVRPKLEANVSLCKELLHSDSPDSHDTEGSAVNSSSDTSLDLGTLCQTTTSPISSKLSAINHVSQAIKSLRWTRQLQSSEQVDAFHDILPDFSKCSCGDPDCIEVCDIRKWLPTSKLDRKLWNLVLLLGESYLSLGEAYKEDKQLHQALNTVELACSIYGSMPQKFEETLFVSSMNKSLSLQSKFHERTQVEDLEAKSGPSDISVEELSSTRLFWAKVWMLVGDIYVQFHILKGQELSRRTKGTTNHLKMQSEVVKEVQRLKKKLTEYSQNCASCSLVNCSCKSDRASSGSSASSSNGSSARTVPHSRKHNRKLQSKNVASKVSRDVEDERVNFKVENKSRKEEEDTSGETKGAVRLEQNESNSKETPGAKKGGIFKYLKGSKTDDAESNLLAALNCYEETRRALQELPSNCSEFQSVLRKKGWVCNELGRNRLGSKELNKAEDAFADAIVAFKEVCDHTNVILINCNLGHGRRALAEEMVPKIEALELHRAFENAYQKALGTAKLEYSKSLRYYMAAKTELSVATAEASSVSDNLKVEVYTQLANTYLRFGMLLANEDTTAAAREQKNILENTHDSSSDGKSSDLRKREVLSASDAIREALALYESLGEIRKQEAAFAYLQLARYHKDCCLGFLETERQGSPRKPESNVIQRAKQYALLADRNWQKSMDFYGPENLPSMFLTILIERSALSSTVSNFWQLNFMLESALSRLLEGRHISKTYAESLRTEDPKLYTKFMAQLQMVLKRMLALSLPSEGANKSQTCGRSGDSGKLRELYKTSLKSTNLCDLNAMHALWTSSP >AT1G30300.1|PACid:19656499 MMESSIPSENGSVTSDRDRSALIFLGTGCSSAVPNAMCLIQRSDNPCYVCSQSLSIPPEKNPNYRGNTSLLIDYCQSDGKHKYIQIDVGKTFREQVLRWFTLHKIPQVDSIILTHEHADAVLGLDDIRSVQPFSPTNDIDPTPIFVSQYAMESLAVKFPYLVQKKLKEGQEVRRVAQLDWRVIEEDCEKPFVASGLSFTPLPVMHGEDYVCLGFLFGEKSRVAYISDVSRFPPNTEYAISKSGGGQLDLLILDTLYKTGSHNTHLCFPQTLDTIKRLSPKRALLIGMTHEFDHHKDNEFLEEWSKREGISVKLAHDGLRVPIDL >AT1G76710.1|PACid:19657324 MQFSCDPDQEGDELPQYEHIYQNDFSYRKHKKQKEEDISICECKFDFGDPDSACGERCLNVITNTECTPGYCPCGVYCKNQKFQKCEYAKTKLIKCEGRGWGLVALEEIKAGQFIMEYCGEVISWKEAKKRAQTYETHGVKDAYIISLNASEAIDATKKGSLARFINHSCRPNCETRKWNVLGEVRVGIFAKESISPRTELAYDYNFEWYGGAKVRCLCGAVACSGFLGAKSRGFQEDTYVWEDGDDRYSVDKIPVYDSAEDELTSEPSKNGESNTNEEKEKDISTENHLESTALNIQQQSDSTPTPMEEDVVTETVKTETSEDMKLLSQNSQEDSSPKTAIVSRVHGNISKIKSESLPKKRGRPFSGGKTKNVAQKHVDIANVVQLLATKEAQDEVLKYEEVKKEAAVRLSSLYDEIRPAIEEHERDSQDSVATSVAEKWIQASCNKLKAEFDLYSSVIKNIASTPIKPQDTKTKVAEAGNEDHIKLLEAK >AT3G44735.1|PACid:19659026 MKQSLCLAVLFLILSTSSSAIRRGKEDQEINPLVSATSVEEDSVNKLMGMEYCGEGDEECLRRRMMTESHLDYIYTQHHKH >AT3G44735.2|PACid:19659027 MKQSLCLAVLFLILSTSSSAIRRGKEDQEINPLVSATSVEEEHDSVNKLMGMEYCGEGDEECLRRRMMTESHLDYIYTQHHK >AT3G61770.1|PACid:19659581 MESLTSNPSFACFSKTISHYPSRFSFVKLTSIQKLEASNNTLSLFCCKSSSNPKPDCNRRIKLNPLCVLRPIIRTIKGLVSSQSRQWMSRFRAYRDDTAAFSEDFAGDLKHNGGLGIALLSVTASAKIKISPFVATLSANPTFVSAVVAWFFAQSSKMVINFFIERKWDFRLLYASGGMPSSHSALCMALTTSVALCHGVADSLFPVCLGFSLIVMYDAIGVRRHAGMQAEVLNLIIRDLFEGHPISQRKLKELLGHTPSQVLAGALVGIVIACFCCQGYLVSV >AT3G58460.2|PACid:19660450 MTYGISSSQKIIQSLRSREESFTVGEKRELFAGVQTRVGQWWNAIPFLTSSVVVVCGVIYLICLLTGYDTFYEVCFLPSAIISRFQVYRFYTAIIFHGSLLHVLFNMMALVPMGSELERIMGSVRLLYLTVLLATTNAVLHLLIASLAGYNPFYQYDHLMNECAIGFSGILFSMIVIETSLSGVTSRSVFGLFNVPAKLYPWILLIVFQLLMTNVSLLGHLCGILSGFSYSYGLFNFLMPGSSFFTTIESASWMSSFIRRPKFIMCTGGNPSSYIPTYSAQNTTSSGFSTGNAWRSLSSWLPQREASNQSSEDSRFPGRGRTLSTARDPTAPAGETDPNLHARLLEDSSSPDRLSDATVNTVADSRQAPIANAAVLPQSQGRVAASEEQIQKLVAMGFDRTQVEVALAAADDDLTVAVEILMSQQA >AT3G14750.1|PACid:19664721 MSGRNRGPPPPSMKGGSYSGLQAPVHQPPFVRGLGGGPVPPPPHPSMIDDSREPQFRVDARGLPPQFSILEDRLAAQNQDVQGLLADNQRLAATHVALKQELEVAQHELQRIMHYIDSLRAEEEIMMREMYDKSMRSEMELREVDAMRAEIQKIRADIKEFTSGRQELTSQVHLMTQDLARLTADLQQIPTLTAEIENTKQELQRARAAIDYEKKGYAENYEHGKIMEHKLVAMARELEKLRAEIANSETSAYANGPVGNPGGVAYGGGYGNPEAGYPVNPYQPNYTMNPAQTGVVGYYPPPYGPQAAWAGGYDPQQQQQQQPPPQGQGHR >AT3G12040.1|PACid:19664981 MKTPARRSKRVNQEESETNVTTRVVLRTRKTNCSKTRAARVRPDYPLTRTTSESEMKLMPPEFFQIDALDLAPRLLGKFMRRDNVVLRITEVEAYRPNDSACHGRFGVTPRTAPVFGPGGHAYVYLCYGLHMMLNIVADKEGVGAAVLIRSCSPVSGMETIQERRGLKTDKPVLLNGPGKVGQALGLSTEWSHHPLYSPGGLELLDGGEDVEKVMVGPRVGIDYALPEHVNALWRFAVADTPWISAPKNTLKPL >AT5G48030.1|PACid:19669587 MVPSNGAKVLRLLSRRCLSSSLIQDLANQKLRGVCIGSYRRLNTSVGNHANVIGDYASKSGHDRKWINFGGFNTNFGSTRSFHGTGSSFMSAKDYYSVLGVSKNAQEGEIKKAYYGLAKKLHPDMNKDDPEAETKFQEVSKAYEILKDKEKRDLYDQVGHEAFEQNASGGFPNDQGFGGGGGGGFNPFDIFGSFNGDIFNMYRQDIGGQDVKVLLDLSFMEAVQGCSKTVTFQTEMACNTCGGQGVPPGTKREKCKACNGSGMTSLRRGMLSIQTTCQKCGGAGQTFSSICKSCRGARVVRGQKSVKVTIDPGVDNSDTLKVARVGGADPEGDQPGDLYVTLKVREDPVFRREGSDIHVDAVLSVTQAILGGTIQVPTLTGDVVVKVRPGTQPGHKVVLRNKGIRARKSTKFGDQYVHFNVSIPANITQRQRELLEEFSKAEQGEYEQRTATGSSQ >AT5G13650.2|PACid:19669692 MELSLSTSSASPAVLRRQASPLLHKQQVLGVSFASALKPGGGALRFPSRRPLPRPITCSASPSTAEPASVEVKKKQLDRRDNVRNIAIVAHVDHGKTTLVDSMLRQAKVFRDNQVMQERIMDSNDLERERGITILSKNTSITYKNTKVNIIDTPGHSDFGGEVERVLNMVDGVLLVVDSVEGPMPQTRFVLKKALEFGHAVVVVVNKIDRPSARPEFVVNSTFELFIELNATDEQCDFQAIYASGIKGKAGLSPDDLAEDLGPLFEAIIRCVPGPNIEKDGALQMLATNIEYDEHKGRIAIGRLHAGVLRKGMDVRVCTSEDSCRFARVSELFVYEKFYRVPTDSVEAGDICAVCGIDNIQIGETIADKVHGKPLPTIKVEEPTVKMSFSVNTSPFSGREGKYVTSRNLRDRLNRELERNLAMKVEDGETADTFIVSGRGTLHITILIENMRREGYEFMVGPPKVINKRVNDKLLEPYEIATVEVPEAHMGPVVELLGKRRGQMFDMQGVGSEGTTFLRYKIPTRGLLGLRNAILTASRGTAILNTVFDSYGPWAGDISTRDLGSLVAFEDGTSTSYALASAQERGQMFVGSGVDVYKGQIVGIHQRPGDLGLNICKKKAATNIRSNKDVTVILDTPLTYSLDDCIEYIEEDELVEVTPSSIRMCKNQKMAKKGRQ >AT5G01030.1|PACid:19670273 MAEKEGKASGTDNDNRVKTKRSSHSRRKECVNKSLEHNDELVKYMSKLPGYLQRIERGEESVHQSNVLNVGVLDWESLQRWKHGRAKGGEISGRSERKVSTIATTSTSGVVVPNDSANRCKIDDQVHTCSNLGKVKASRDLQYSLEPQLASRDSLNKQEIATCSYKSSGRDHKGVEPRKSRRTHSNRESTTGLSSEMGNSAGSLFRDKETQKRAGEIHAKEARERAKECVEKLDGDEKIIGDSEAGLTSEKQEFSNIFLLRSRKQSRSTLSGEPQISREVNRSLDFSDGINSSFGLRSQIPSSCPLSFDLERDSEDMMLPLGTDLSGKRGGKRHSKTTSRIFDREFPEDESRKERHPSPSKRFSFSFGRLSRNFSLKDISAGQPLSSSEDTIMSGSMRFDGSVCPSQSSNPENQNTHCRSRVSPLRRFLDPLLKPKASESVLPSKARSSSSNPKPITNSNVPLQDEKKQDASRTLAIFQLTIRNGIPLFQFVVDDNSSSSRSILGATMKSSDSSFKDDSVQYCTFYSVNEVKKKKSGSWLIHGHREKHCGFVYNIIGQMQLGNSMSVDISEQKSLITESVLFDESEQVKGRKEVAAVVIKKKPVEGSYTSFEETSVIIPGGVHSFPEKGAPSPLISRWRSGGLCDCGGWDVGCKLHVLSNKTVLHKFNQSFTLFDQEVSEQDSSPALAMTELKTGIYRVEFGSFVSPLQAFFVCVTVLTCASKAKTTGKSSSPMAPPLSPVGRV >AT5G16780.1|PACid:19670576 MEVEKSKSRHEIREERADYEGSPVREHRDGRRKEKDHRSKDKEKDYDREKIRDKDHRRDKEKERDRKRSRDEDTEKEISRGRDKEREKDKSRDRVKEKDKEKERNRHKDRENERDNEKEKDKDRARVKERASKKSHEDDDETHKAAERYEHSDNRGLNEGGDNVDAASSGKEASALDLQNRILKMREERKKKAEDASDALSWVARSRKIEEKRNAEKQRAQQLSRIFEEQDNLNQGENEDGEDGEHLSGVKVLHGLEKVVEGGAVILTLKDQSVLTDGDVNNEIDMLENVEIGEQKRRNEAYEAAKKKKGIYDDKFNDDPGAEKKMLPQYDEAATDEGIFLDAKGRFTGEAEKKLEELRKRIQGQTTHTFEDLNSSAKVSSDYFSQEEMLKFKKPKKKKQLRKKDKLDLSMLEAEAVASGLGAEDLGSRKDGRRQAMKEEKERIEYEKRSNAYQEAIAKADEASRLLRREQVQPFKRDEDESMVLADDAEDLYKSLEKARRLALIKKEEAGSGPQAVAHLVASSTNQTTDDNTTTGDETQENTVVFTEMGDFVWGLQRENDVRKPESEDVFMEEDVAPKAPVEVKEEHPDGLTEVNDTDMDAAEDSSDTKEITPDENIHEVAVGKGLSGALKLLKDRGTLKEKVEWGGRNMDKKKSKLVGIVDDDGGKESKDKESKDRFKDIRIERTDEFGRTLTPKEAFRLLSHKFHGKGPGKMKEEKRMKQYQEELKLKQMKNSDTPSQSVQRMREAQAQLKTPYLVLSGHVKPGQTSDPQSGFATVEKDVPGSLTPMLGDRKVEHFLGIKRKSEPGNSDTPPKRPKP >AT5G13640.1|PACid:19671151 MPLIHRKKPTEKPSTPPSEEVVHDEDSQKKPHESSKSHHKKSNGGGKWSCIDSCCWFIGCVCVTWWFLLFLYNAMPASFPQYVTERITGPLPDPPGVKLKKEGLKAKHPVVFIPGIVTGGLELWEGKQCADGLFRKRLWGGTFGEVYKRPLCWVEHMSLDNETGLDPAGIRVRAVSGLVAADYFAPGYFVWAVLIANLAHIGYEEKNMYMAAYDWRLSFQNTEVRDQTLSRMKSNIELMVSTNGGKKAVIVPHSMGVLYFLHFMKWVEAPAPLGGGGGPDWCAKYIKAVMNIGGPFLGVPKAVAGLFSAEAKDVAVARAIAPGFLDTDIFRLQTLQHVMRMTRTWDSTMSMLPKGGDTIWGGLDWSPEKGHTCCGKKQKNNETCGEAGENGVSKKSPVNYGRMISFGKEVAEAAPSEINNIDFRGAVKGQSIPNHTCRDVWTEYHDMGIAGIKAIAEYKVYTAGEAIDLLHYVAPKMMARGAAHFSYGIADDLDDTKYQDPKYWSNPLETKLPNAPEMEIYSLYGVGIPTERAYVYKLNQSPDSCIPFQIFTSAHEEDEDSCLKAGVYNVDGDETVPVLSAGYMCAKAWRGKTRFNPSGIKTYIREYNHSPPANLLEGRGTQSGAHVDIMGNFALIEDIMRVAAGGNGSDIGHDQVHSGIFEWSERIDLKL >AT5G27660.1|PACid:19673236 MMNFLRRAVSSSKRSELIRIISVATATSGILYASTNPDARTRVSLAIPESVRESLSLLPWQISPGLIHRPEQSLFGNFVFSSRVSPKSEAPINDEKGVSVEASDSSSKPSNGYLGRDTIANAAARIGPAVVNLSVPQGFHGISMGKSIGSGTIIDADGTILTCAHVVVDFQNIRHSSKGRVDVTLQDGRTFEGVVVNADLQSDIALVKIKSKTPLPTAKLGFSSKLRPGDWVIAVGCPLSLQNTVTAGIVSCVDRKSSDLGLGGKHREYLQTDCSINAGNSGGPLVNLDGEVIGVNIMKVLAADGLGFSVPIDSVSKIIEHFKKSGRVIRPWIGLKMVELNNLIVAQLKERDPMFPDVERGVLVPTVIPGSPADRAGFKPGDVVVRFDGKPVIEIMDDRVGKRMQTCETRRRLRQFCNGNFTIFNQMC crb-blast-0.6.4/test/query2.fasta0000644000175000017500000002413112577436147016555 0ustar mcrusoemcrusoe>scaffold24621 AAAAAGCACACTCAAAAGACATCAGCTTTTATTTCCCTGTCTGTCTGCCATTAATTCCCATAAATATAACACATCACATCTCTCTGCTCCTCCTTTCCCCTTAAAACCAGAGACCCTTTTCTCACCATAACATCTCTCTCTCTCTCTCTCTCTCTCTCTCATGGACTCTCATCATACCTTCATATAACCTTCATTTACCCCCAATTCCCCACCTGGGTTTTCTTCTTCACCATCTTCCTTCACCTGGGTCATCTTCCAATTTCACAATATGATCACTGGTTCCGACCTTTACCATGTCTTTACGGCCGTGGTTCCACTCTATGTCGCCATGATCCTAGCCTATGGCTCGGTGAAATGGTGGAAGATCTTCACCCCTGATCAATGCTCAGGGATCAACAGATTTGTAGCTCTATTTGCTGTCCCATTGCTCTCCTTTCACTTCATCTCAACTAACAACCCTTACACCATGAACTCTAGGTTCATCGCTGCTGACACCCTCCAAAAACTCATCGTTCTTGTGGGTCTAGCCTTCTGGTCAAGATTGAGCGCTAGAGGCTCGTTAGAATGGTCCATCACTCTGTTTTCGTTGTCAACACTCCCCAACACACTTGTGATGGGAATCCCTCTTTTGAAAGGGATGTATGGTGACTTTTCAGGGAGTTTGATGGTGCAGATTGTGGTGCTTCAGTGCATCATCTGGTACACTTTGATGCTGTTTCTGTTTGAATACAGAGGTGCAAGATTGTTGATCGCTGAGCAGTTTCCAGACACTGCTGGTTCGATTATTTCTTTTAGAGTTGATTCTGATGTGTTGTCGTTAGATGGTAAAGAGCCATTGCAGACAGAGGCTGAAGTTGGGGACGATGGGAAGCTTCATGTGACTGTTAGGAAGTCTGCAAGCTCTCATTCGGAGATCTTCTCACGGCGTTCACACGGGGGAATGAACTCCGGTGTGTCATTAACCCCTCGTCCGTCAAACTTAACAAATGCTGAAATTTACTCTTTACAGTCGTCAAGAAACCCTACCCCAAGGGGCTCGAGCTTCAATCACACTGATTTTTACTCAATGGTTAATGGGAAAAGTGGTGCTAGTCCTCGTGGGTCGAATTTTGCAGGGTATGATGAGGAAAGTGGGAGTAATGTGAAGGTGAATGGGGGTCATGGGGGTGCAGGGTACCCTGCTCCTGCGAATGCCGGAATCTTTTCTCCGGTGGGTGGGAAGAGAGGTGGCGGCGGCG >scaffold46687 AACTTAAGCTGTACAAAAATGTTTGCACTTACAAGCATGCAAGAACATAAAATATGTCTTGGAGTGTAGAGATCAATTTGTTATGCCTGATTGCCTCAGACGAGATGAAGTGTGAGAAATTGTGTGCAACAAACTCATCTATAGACTATACACATGCAATTTGTAGGCGTCCAAATTTTTTATGCTAAGCACTCTTATAAGAGCAACTCCAACATAAACAAGCACAAAAAATCTTTCATGTTACATGTCCCAGCATTTATACATGTAACATCCAATACTAGCTAGTTAGATCTTGGGCTGCAAATATTTTTATTAATTGCAGTGCCACAATTCACCCTTGCATCACTCAGTTCTATGATATATTAATCTTTTTATCTTGTTATCATGCTGATATCATTAATTCACCTTTTAATTCAAGAGGAGCAGGAGATCCATCAAGAAGCACAAGGAACAGATGAAATAAGAGAAACNGCACAAGGAACAGATGAAATAAGAGAAACAAACTCTAGTATTAAAAGAACAAGAATAATGCAGGTTTTATCAACTGTTGGGAAGAAGCTTCTAATTAATCCAAATTCTCATGCAACTGTAGCAGGCCTTTCATGGGCATTCATAAGCTTCGGGTAAGTGTGCATAAATACCGTCAGCACAAAGAATACAATTGCATAGATAATAATACAATAGTTAAATATAATGCAGGTGCAATGTAAAACTGCCAAAGGTATTTGAAGATTCAGTATCTATAATATCAGAAGGAGGACTTGGAATGGCAATGTTCAGCCTAGGTAACAACATAAATTTAAGCCGTTTCTAGCAAGTGTGAGAATATTTAAAATATAAATAATAGAAAATAAAAAAGATAAAATTTTATATTATGTGTATCACTCTACAGGTCTATTCATGGCATCACGGACACGCATAGTAGCTTGTGGTACCCGATTGACATTAATGGCCATGGTCTTGCGGTTCATTGTAGGGCCCGCCATAATGGCAGGGCCGTCTGTTGCTATTGGATTAAAGGGCATACCATTGGAAATTGCAGTTATACAGGTAGAAGTGTAGAACCATGTTTTCTATTAATATTAGTATTATTGTTATACCAACAAGACAAATACAAACCAATTAAAAACTACTATTTCCTCCAGGCAGCTCTTCCTCAGGGTATCGTCCCATTTGTATTTGCCAACGAGTATAATGTTCACCCAGAAATCTTGAGCACCAGGTGTTAACAGTGGTTGATTAATATTAATACCTAAACTTCAATTCACAACATGACAATTGACTACTTTTGATTACAGCATAATCATCGGATTGCTTGTTGCGTTGCCTATTGCACTGGTCTACTACTTCTTGTTGAGATTATAAAAAATACACGAAAAACAAACAGTGAAGCAGTTGAATGTGACGCATATATGGATTTTCATATTTCTTTAATAGCCTGATATAACAACTTCAAACTTACGAAAATTCTTTTATAAAGCCAATGCATTGTGCATATACAGCTAACTAGAAGATGATTCGTTCAAGCAAATGATAAAAAGCTAGAAGGCACCAAGATCTTTCAAGCCCAGGAATTAGAACACATCAGCATGATATCTTGTCATTTGAGTATGCTTCATTTTATTTATTTATTTTTTCAATTAAACATATATGTAGCTACAGGTAAATTGTATATAAAAAGCATATAAACAACTAAACAAGTACATAACTTTCTTTTTATAAAGTGTGTGACTATCATGTGTAACATTGTGCTATGCATCTACAAAATTGCAAAGTTCATGGTACCTCCAAATAACCACCATTTTACAAGATCGTAGTTGGATTAACATTTTATCTATGAACCTAGTTCAAATATTCCAACAATCGTATATATACAACAGTTTCATTTCATTCTAGAAAACAGCTACAGTTAGCACCTTGTAATAAAGGGTTAAAGATCACTACAAGGTTACATAAATGTGAAATCAACTCACAACTCATCACTGTAATATGGAAAACAAATGTGAATGCACGATTACATAATTACACAAACTTTAACAAAACCAAAACATTCTGGAGTTCATGGTAAATATGCTCATG >scaffold47909 TTTTTTTAAATGAAATTTAGAAAAACAACCAAAATGTTTTAAAAAAAATTGAAAAACTAAATAATAAATTCCTTACATTAGTTGATTATCATTTAACATCTTCTTTTGTAATTGATTTTGTTTCAATTCAAGTGTTTTCTAAATATATTAAAACATCATCATTCAATTGAATGTATGTCATGTACTGGTTGTAGGTAAAAAACACAAAAGATAACCTAACCATAAACATGCGTTTAATTAAGCATCTTTTTTACTTTTGAGACGTTTATAAAAGGTAAATAAAAAACATAAAGTTAATCACACTTATAAGTGTCAGTTGACCCTCTTTTTTTTTATGTTAACATGCTCACACTGAGATGTCCTTTCTGTTTGAAAAAATAAAGATATAAAGGTAGCTACCTTAACATACAAATTCTTCATTCATTGTCAAGCACCGCAGCATTTAATTTGAAAGCACTGCACCATGATCACTGTTTCAGATTTCTACCATGTGATGACCGCGGTGGTCCCGCTCTACGTCGCGATGATCCTAGCGTACGGCTCGGTGAAATGGTGGAAGATCTTCACCCCTGATCAATGCTCAGGCATCAACCGCTTTGTCGCCCTTTTCGCCGTCCCCCTCCTCTCCTTTCACTTCATTTCCTCCAACAACCCCTACAAAATGAACCTTCGCTTCATCGCGGCCGACACGCTCCAAAAACTAGTCGTCCTCGCGGTCCTAGCCGCGTGGAGCAACCTTACTAAAAGGGGTAGTTTAGAATGGTCGATAACATTTTTTTCACTTTCAACTTTACCAAACACGTTGGTTATGGGAATCCCTTTGCTTAAAGGGATGTATGGTGGTGAGTCTGGTAGCCTAATGGTCCAAATTGTTGTTCTACAATGCATTATTTGGTACACTTTGATGTTGTTTTTGTTCGAGTTTCGCGGCGCAAGGTTGTTGATATCCGAACAGTTCCCTGGCACCGCGGGGGCTATCGCCTCGATTCATGTCGATTCGGATATCATGTCGTTGGACGGACGGCAAGTGTTGGAGACCGAAGCCGAGGTTAAAGAGGACGGAAAGCTTCACGTGACGGTCCGCAAGTCGAATGCGTCGAGATCCGACGTGTTCTCGAGAAGGTCGCAGGGGTTTTCGTCTACGACCCCTCGGCCATCGAATTTGACGAATGCCGAGATTTACTCTCTGCAATCGTCTAGAAACCCTACCCCTAGAGGGTCGAGTTTTAACCACAATGATTTTTATTCTATGGCGGGTGGGGTTGGTGGTAGGAATTCCAACTTCGGGGCGTCGGATGTGTATGGGCCTCCTGTATCCAGAGGGCCCACGCCCCGTCATTCCAACTATGAAGAGGAAGGTAGTGGGAATAATGCTAACAAGTCTCGTTTTCATCATGGAGGAGTGCTGGGTGGTAATAACTACCCAGCACCAAATCCCGGGATGTTTTCTCCGTCAACGGGAAAACCCAGCATACCGTTAACCAGAAAGGCAAACGGGCAAAAAGCAGATGAAGGTTCAAATGATCTACACATGTTTGTTTGGAGCTCGAGTACTTCTCCGGTTTCCGATGTATTCGCGGCTCGTGAATACGGAGCACTCGACCCACCAACCACAAAAGATTTAAAAGTTCCGATATCACCCGTAAAAGGTAACGGAGAAGAGTACTTGGAGAGTTACGGAAATAACAACATAAATATTGAAGGAACGGGTACAGGCGTCAAGTCAATGCCGCCAACGAGCGTGATGACGAGGCTAATACTGATAATGGTGTGGAGAAAACTCATCAGAAACCCGAATACTTATTCGAGCTTGATCGGTCTAGTCTGGGCTCTAGTATCTTTCAGATGGAATGTTGATATGCCTGCAATTATAGCAAAGTCCATTTCAATATTATCTGATGCTGGGCTTGGAATGGCCATGTTCAGTCTTGGTTTGTTTATGGCATTACAACCAAAGATGATAGCATGTGGAAATTCTGTGGCAGCTTTTTCGATGGCTGTGAGATTCCTTATAGGACCGGCTGTCATGGCAGTCGTTTCTATCCCTGTTGGCCTACGTGGCGTCCTATTACGCATTGCCATTGTCCAGGCTGCTTTACCACAGGGTATTGTCCCCTTTGTGTTTGCCAAGGAGTACAACGTCCACCCTGATATCCTTAGCACTGGCGTTATATTCGGAATGCTAATAGCGTTACCCATCACGCTCGTATACTACATTTTGCTTGGGCTAGAGAAATAGGTAATGTTTACATCATAAATTTGGTGGAAAATACGTCCATACTCATGCTCAAAAGCAATATTGTCTATGTAGTTTTCGGGTTTTTGGTTGGTAGAAAGAGAAAAAAATGGTGGTTGCTTAAATAGGATCCATTTTACATTGTTTAGCCGAGTTAATGTTATACGATTAAATGTTAAACTCGCCTTTTTTAATGTAGCTTATGTATTTATGTTGTATTTCATCATTTACATGCCAATTGAAACATTTAGATATAAAATACTTACGGT >C612630 GTGCGCTTTTTTATAACCAAGAAATATATAATAATCAAAGTGCCTTTTCATGAAACATTAATACCTGGACAATTGCAATGCGTAAAAGAACGCCACGTAGGCCAATTGGATAAGAAACGATCGTCATTACAGCTGGTCCCACAAAGAATCTCACACCCATTGCCATTGTTGCCATGGAATTCCCGCATGCTATGATCCTTGGTTGTAATGCCATAAACAAA >contig-4577 283 0 CGCTCGTTGGCGGCATTGACTTGACGCCTGTACCCGTTCCTTCAATATTTATGTTGTTATTTCCGTAACTCTCCAAGTACTCTTCTCCGTTACCTAAAGTACGTAAACGTAACATTTTATCGATCAGCTTAAATCTAAAAAGATAACGACAATGAAAATATTCTTAGATATATAAAAGTTGACCGGCCTTTTACGGGTGATATCGGAACTTTTAAATCTTTTGTGGTTGGTGGGTCGAGTGCTCCGTATTCACGAGCCGCGAATACATCGGAAACCGGAGAAG >contig-69208 224 0 ATTTGCGCCACTTTCGACTCATTTTACCCGTTCCCTTTAAAGTTGCATATTTTTATTTGAGCCATTTAGACCGTATTACATAAAACACAACCCAAATAGACCCATTTATTCAAAACTGCCACCTCTATTTTCATTTATACCTAGACTAAACATAGCCATTCCTAGGCCTGCATCCGAGAGAATGGTAACTGAATTTTCGAGAATCTGTGGTTTCTTTATTCCCC >contig-115072 367 0 GGTTGATACTGATCATGGTGTGGCGGAAACTTATCCGGAATCCAAACACATACTCGAGCCTCATTGGTCTAATATGGTCTCTTGTCTCGTTCAGGTAAATGGTTATGATATAAATATGTAGATTCAGGTAAATGATTATGATATAAATATGTAGATTTAAAAGTAGATTTAATACGTGTTCATATGTTAGAAGTTAAAAAAAACAATTATTAAAGGATAATGTTTTTAAATATATAGAATAAATATTTGTTTGTTAATAAATATATGTTTAATGGTGACAGATGGCATGTGGAAATGCCAATAATAATAGCAAAATCAATCTCAATACTTTCGGATGCTGGTCTTGGAATGGCTATGTTTAGCTTAG >contig-1453 255 0 TAGCCATTCCTAGGCCTGCATCCGAGAGAATGGTAACTGAATTTTCGAGAATCTGTGGTTTCTTTATTCCCCACCTGCATATATCATGAAGAAAAGAAACAAAAGTTAAAACATTTTTGATCTTAATCTTTAATAGCATAAACCCATGTGAATCAAGTGGTAATCACCTGCAAGCAGCCAAAGCCCAGCTCAAACCAAGTATGCTTGCATATGAATTCGGGTTCTTCACTAGCTTAATGCATACCATTTTCAAGA >_47104 CTAGTTAGATCTTGGGCTGCAAATATTTTATATTAATTGCAGTGCCACAATTCACCCTTGCATCACTCAGTTCTATGATATATTAATCTTTTTATCTTGTTATCATGCTGATATCATTAATTCACCTTTTAATTCAAGAGGAGCAGGAGATCCATCAAGAAGCACAAGGAACAGATGAAATAAGAGAAACAAACTCTAGTATTAAAAGAACAAGAATAATGCAGGTTTTATCAACTGTTGGGAAGAAGCTTCTAATTAATCCAAATTCTCATGCAACTGTAGCAGGCCTTTCATGGGCATTCATAAGCTTCGGGTAAGTGTGCATAAATACCGTCAGCACAAAGAATACAATTGCATAGATAATAATACAATAGTTAAATATAATGCAGGTGCAATGTAAAACTGCCAAAGGTATTTGAAGATTCAGTATCTATAATATCAGAAGGAGGACTTGGAATGGCAATGTTCAGCCTAGGTAACAACATAAATTTAAGCCGTTTCTAGCAAGTGTGAGAATATTTAAAATATAAATAATAGAAAATAAAAAAGATAAATTTTTATATTATGTGTATCACTCTACAGGTCTATTCATGGCATCACGGACACGCATAGTAG >_47472 CAAGAGAATTACTAACATGAAATTAGAATATGCAACCTTTTTAAGTTAAAAGCATGTTGCTTTTGGTTTTACAAGTTTCTTTTAGCCCACTTACAAATGAGAATCAACTTGTCACATTCACACCATTAGGACACTTAAGTAGTCAATAACCCTTGAAAGCTTTACATCATATTTAATTAAAAACCTTAAATAATTACATCAAAAGAGATGATGCACATGCCACAAACAAACAAGAACCCAAATTAATTAAAAACATAGCTCTCCTTCCCATCAATCCTAATTGTTTTCCTAATATATCACTAAGATTTTTCTTTTTTTCCCCAAAAAAAGAAGAAAAAAAAAAGATTAAATTCCCTTCTTTTGCTCATGTTTGTCTCTCCCTCTTTTAAACTATATCCTTCTTCCTTGCTTTCTTCATTTCTTGAGAATCTACACATTAAAAGATACAACATTGGGAGATGGAGGTAGCACGATCCTTACATCAAGTCAAAAATTCCTTATTCCAATTGTCTTGGACACTTCATAAATTTTTCATTTTTCGATCTTCACAATCCAAGAACGATGTAGTAGACTAGAGTTATCGGTAACGCTATCAACATCCCGAAAATAACC >_77170 AGCTCTGCCTCAAGGAATTGTCCCTTTTGTGTTTGCTAAAGAATATAATGTCCATCCAGATATACTTAGCACAGGGTGAGTTTTTACTGGCTTTACATATCTTATGTCTTACTTTTGCGCTTTTGTAACTTGCACATCATGCATATGAAAGTTGTACATTGTCATATGTAACAAAGCATCAAATGGTCATGTTTGAAGAGCAGAGATCCGTTGCAACTTTGCCATGCCTACTTTGTATCTTATGCATCAAAAGTTGTACATTGCTCCAAACATGCAATGCTTGTCAAAGAGTATAAGTAGCATCTTGATTTGAAAATTTACAAATCTTTAATACATGGTTTACATGTTTGTGTTGCAGGGTTATATTTGGAATGTTGATAGCACTACCAATAACACTGGTGTACTACATAGTGTTGGGGCTTTAAATGAGTGG >_88236 TTTTTGTGCTAAAGAAGTAGACGCAACACTACTACTTTCTTTTCTTTTCATGGGAGAAGAATATACACAACACAACACAACACAAACAACAATTGGAGAGACAACAAAACAAACATTGATTTTACTTTACTTCCTGCCAATGTCTTCTTGTCAAATTACAATTCTCTCCCTCCCAACAATGACCCTCCCTCTCTAATGTCATCTCTTTTTACTCTCCACTAAAGTTAACAAAATGGTCATTTCACATGTTAGACAACCACAACCCAAAACAAACTTAAAACTTCAATTCTTCAAACAAGACAAGAGTCAAAGCCCACTCATTTAAAGCCCCAACACTATGTAGTACACCAGTGTTATTGGTAGTGCTATCAACATTCCAAATATAACCC >_93178 TATAAAATAAAACATAAGATAAACTTAAGCTGTACAAAAATGTTTGCACTTACAAGCATGCAAGAACATAAAATATGTCTTGGAGTGTAGAGATCAATTTGTTATGCCTGATTGCCTCAGACGAGATGAAGTGTGAGAAATTGTGTGCAACAAACTCATCTATAGACTATACACATGCAATTTGTAGGCGTCCAAATTTTTTATGCTAAGCACTCTTATAAGAGCAACTCCAACATAAACAAGCACAAAAAATCTTTCATGTTACATGTCCCAGCATTTATACATGTAACATCCAATACTAGCTAGTTAGATCTTGGGCTGCAAATATTTTTATTAATTGCAGTGCCACAATTCACCCTTGCATCTCTCAGT >_123423 CGAAACGATATTATTTGAGGAGTAATATAAAAATTTTTAATAATATAATTTAAAAAGTTGTATACATTAAAAATTGACATTTGCGCCACTTTCGACTCATTTTACCCGTTCCCTTTAAAGTTGCATATTTTTATTTGAGCCATTTAGACCGTATTACATAAAACACAACCCAAATAGACCCATTTATTCAAAACTGCCACCTCTATTTTCATTTATACCTAGACTAAACATAGCCATTCCTAGGCCTGCATCCGAGAGAATGGTAACTGAATTTTCGAGAATCTGTGGTTTC >_157256 TGCTTCACGGTCCACTCCATTCGGGCCCGGTTGGTTCCCAAAGCTAAACTCATTCCGGCCAAAATCATCATAATCTTTAGTATGGGGCACCCCTCCGAGATCATTACCATACTCCCCACCTCTAAACACATGAATACCACCTTCTGATACAGGTGAAGCACTAGAACTCCACACAAACATATGAAGATCTTTACCACCACCACCACCACCACCACCGCCGCCGCCAAGATCGGGTTTT crb-blast-0.6.4/test/query.fasta0000644000175000017500000003711312577436147016477 0ustar mcrusoemcrusoe>scaffold3 CCACCCCACTTCAACTCCCAACAACATATATACATTACACACCCCCACAACACACTCACACACTCTCTCACACAACACCACCAGACAATGAACCACAACTACCGTTACAATGTTCTTCTTTTCTTCTTCCTCATCATCTTCTCACATACATCTGCTCATCGTTTCTTGCACACCAAATCAGGTGAAAGCATGGTGAAACCCGATGATNCCAGGTGAAAACATGATGAAACTCGATGATCAATCCATCAATTACACCGGTGAAAACCCTCTTGTCGAAGTAGAAATAGTCAACTCTGACTCCTTCAATGAGGTTATGGGGGTGGAGGACTGTGGGAGTGGAGATGAAGAGTGTTTGAAGAGAAGGGTGCTTGCAGATGCTCATTTGGACTATATTTACACTCAGCATCATAAGCATTGAAATAAGTTGTATTTCACCCTCTTTATTTATAGCTTTTTATGTCTTAATGTAACATAGGGTTAAATTCAAGTAATATTAATGAAATAAAAAAAACTTACTTAGATTGATGGTTGGATTTAACATTTAATTAGTTATACTTATTTTACTTATATTGAAGTGGATAATTATACTATCTTATACTGTATTATACTCGAAAAAAAGAGGTTTTTGGACTTGGGGTCTCAATAAGTGCAGCCTCAAATAGATGTGTCTCATCAGACCCTCTCTAGACCTTATAAATAGCATTGTTATAAGTGAGATTATACTGTGTTTGTTTGTTTGTTTGATTCATAGACAAGAACCAGTTTATATGCAAGAAATTGGTCATAGGATGAGCAAATTATCAAACTGGTCCGTAACCAGCCGGTTTAAATTATGGGAAACAGTCCAAAACAGGTATATATAACCGGACTCCAACCAGTCTCAACAGCAGGTCCTTTCGGGTTCTGAAAACACTGTTAAAAAGGATAATTACATGGTCGGGACAGTAATTGAGTAGAGCTACCAATAATTCCATGTTCATGAACACTAACATTGAGTAATTCTT >scaffold4 CCACCCCCCCACTTCAACTCCCAACAACATATATACATTACACACCCCCACAACACACTCACACACTCTCTCACACAACACCACCAGACAATGAACCACAACTACCGTTACAATGTTCTTCTTTTTTTCTTCTTCCTCATCATCTTCTCACATACATCTGCTCATCGTTTCTTGCACACCAAATCAGGTGAAAGCATGGTGAAACCCGATGATNCCAGGTGAAAACATGATGAAACTCGATGATCAATCCATCAATTACACCGGTGAAAACCCTCTTGTCGAAGTAGAAATAGTCAACTCTGACTCCTTCAATGAGGTTATGGGGGTGGAGGACTGTGGGAGTGGAGATGAAGAGTGTTTGAAGAGAAGGGTGCTTGCAGATGCTCATTTGGACTATATTTACACTCAGCATCATAAGCATTGAAATAAGTTGTATTTCACCCTCTTTATTTATAGCTTTTTATGTCTTAATGTAACATAGGGTTAAATTCAAGTAATATTAATGAAATAAAAAAAACTTACTTAGATTTTTGATGGTTGGATTTAACATTTAATTAGTTATACTTATTTTACTTATATTGAAGTGGATAATTATACTATCTTATACTGTATTATACTCGAAAAAAAGAGGTTTTTGGACTTGGGGTCTCAATAAGTGCAGCCTCAAATAGATGTGTCTCATCAGACCCTCTCTAGACCTTATAAATAGCATTGTTATAAGTGAGATTATACTGTGTTTGTTTGTTTGTTTGATTCATAGACAAGAACCAGTTTATATGCAAGAAATTGGTCATAGGATGAGCAAATTATCAAACTGGTCCGTAACCAGCCGGTTTAAATTATGGGAAACAGTCCAAAACAGGTATATATAACCGGACTCCAACCAGTCTCAACAGCAGGTCCTTTCGGGTTCTGAAAACACTGTTAAAAAGGATAATTACATGGTCGGGACAGTAATTGAGTAGAGCTACCAATAATTCCATGTTCATGAACACTAACATTGAGTAATTCTTGTACTGCA >scaffold5 CCACAAACAAGATTTGTTTTAAAGAAAGCTCTTGAATTCGGTCATGCAGTTGTTGTTGTTGTGAATAAGATTGATAGACCGTCTGCTCGCCCTGAATTCGTCATCAATTCTACTTTTGAACTCTTTATTGAACTCAATGCATCTGATGAACAATGTGATTTTCAAGCAGTGTATGCTAGTGGTATAAAGGGAATGGCTGGACTTTCTCCTGATAATTTAGCAGATGATCTTGGACCACTTTTTGAGACAATAATTAGATGCATACCCGGGCCACGTGTTAAGAAGGATGGCGCACTTCAAATGCTTGTCACGAGCACAGAATATGATGAGCACAAAGGAAGAATAGCGATTGGGAGGTTACATGCCGGTATTTTGAGTAGAGGCATGGATGTTCGTATATGCACACCAGATGATGCATGCAGATTTGGGAAAGTTAGTGAATTGTTTGTANGATTAGTTTCTGTTATGTAAAATGTGTAACAGATTGTGTTCTTATGTTTTGTTGGCATAAGCTCAGATATGCACACCAGATGATGCATGCAGATTTGGGAAAGTTAGTGAATTGTTTGTATTTGAGAAGTTCTCTAGGGCACCTGCAGAGAGTGTTGAGGCGGGTGATATTTGTGCCGTGTGTGGTGTTGGTGATGTTTAGATTGGAGAGACCATTGCTTGTAAAGCTGATGGGAAACCTTTGCCTGCAATAAGTGTTGAAGAGCCTACTGTAAAAATGGCTTTCTCTATCAACACTTCACCCTTTGTTGGTCGTGAGGGGAAGTATGTTACAAGTAGAAATTTAAGAGACAGACTGTACCGTGAGCTGGAGAGAAATTTGGCCATGAAAGTAGAAGATGGTGAAACCGCTGATACTTTTCTTGTTAGTGGACGTGGTACTTTACATCTCACTATACTGATAGAAAACATGCGAAGGGAAAATTATGAGTTCATGGTTGGCCCTCCAAAAGTAATTAACAAAAAAGTCGATGATAAGGTTCTTGAACCTTATGAGATTGCGACCGTAGAGGTGCCTGAAGAACACATGGGCGCAGTTGTTGAACTTTTAGGTAAAAGGCGTGGGCAGATGTTTGATATGCAAGGAGTTGGCTCTGAAGGAACTACAGTATTGAAGTACAAGATCCCTACTCGTGGACTTCTTGGACTAAGAAATGCCATTCTAACGGCTTCCCGAGGAACGGCTGTTCTCAACACGATCTTTGATAGTTATGGGCCTTGGGCTGGCGATATGACAACCCGTGATCTCGGATCCCTGGTTGCATTCGAGGATGGGACCTCGACGTCATATGCTCTTGCTAGTTCTCAAGAAAGAGGGCAGTTGTTTATAAAACCCGGAGTAGAAGTTTACAAAGGTCAAATTGTTGGCATTCATCAACGACCTGGTGACTTGGCGCTCAATGTATGCAAAAAGAAAGCAGCTACTAACGTCCGCTCCAATAAAGAAGTGTCAGTTGTTCTTGATACACCATTGGATTATAGTCTTGATGATTGCATTGAGTACATCCAAGAAGACGAGTTAGTTGAAGTAACTCCAAAAAGTGTTCGGATGTGCAAAAACGCGAAGATGAACAAAAAGGGCCGGTAAACAAGATCTTTTGATGGCACATTTCAGTGATCAACTTAGATCTTGAGCAATTTTTGCACCAATATAAACCATATGGTGCTGGCTACGCGAAGTATTAGGTGATGAATATAGAAGATTTTTTAGTTCTTAAAACATAAAAATAGTATACGGTTATGCAGACGGCACAGTGATCATCGATCATATCGACTTATATACGATAATCACGTAAAAAAAATCAATATTTAATAGCGGGTCGTGGTGAAGAATCGATGTTAAGAACTACACATGAGTGTATCTTGACTCATACAGGTTGTCTGTACTTTGTAACATCATATATAGTTGTGGCCAAACACCACACTGATGATGCATTTTTGACTTCCTCATATTTACCATCTATAGCAATCCCTTCACCATTTCTCACAGCCAAAGATCTCAAAAATAAAAAAAAAAATATTTTAAATTTGTGTTTTCTTCAAAGTTTTTAGTGTAGACATATGCTTGTATAATTGGTATTAGAATATTTATCAAAAGAATATTTGTTGGCG >scaffold19 CTGTTGGCTACAAGTAGTGCTATATTTCACCTTTTAATTACATTGATAGCTGCCTTCAACCCAATTTATTCGTATGATCAATTCATGGACGAGTGTGCAATTGGCTTCTCTGGTGTTCTATTCTCTATGATTGTTATAGAAACAAGCTTAAGTGGAGTCCAATCTAGAAATGTATTTGGACTTTTTAATGTACCTGCTAAGTTGTATCCGTGGTTGTTATTGGTGCTGTTCCAGCTTCTTATGACAAACATCTCATTACTCGGACACTTATGTGGGATTCTATCTGGATTTGCATATACTTATGGATTATTCAACTTTATAATTCCGGGCAGCTCGTTCTTTTCAGGCATAGAATCAGCTTCTTGGCTTTCAACTTGTGTGCGTAGACCAAAATATATAATGTGCACAGGTGGTGATCCTTCTGGATACATCCCTACATATTCTACTCGTAACACAACATCTAGTGGAACTCTTTCCGGGAATATGTGGACAAACTTGTCGTCATGGATTCCACGTAGAGAGGTGCTTCCCCAGTCAACAGAAGAAAATAGCAGGTTTCCTGGGCGTGGGAGGACACTTGGTGCAACTCAAACC >scaffold27 TATTTTCCCAAAAGGTTACAAAAGTATTTGATAATAACATAAAAATTAACCATATATGTGGTGAAGATTAGCCCAATGGGTACACCAGTGGTGAAGATCAAAGGTTAAGTTGTAACCTCAAAACCCATCTCCCTATCCAAATCCTTTAAACCAGTGGTCAATATTTCACAGCCATGTGGCATCACAGGCAATCTCAATTGTGTGGTGGTTAACAATTCAAAAGCTAATCCTCTCTATATAAGTTATTATCTTCNCTTCACAGTGTACCTTCGTATCATTCCTAAATTCAACTTCAGTTCCACTGACACTCGCCTGAGATCAATGGCAACCGCCGTCTCTACCGTCGGAGCCGTCAGCCGTGTTCCGTTGAGCTTGAATGGAACCAGTGGTGGTGCTGCAGTCCCAAACTCAGCTTTCATGGGCAACAGCTTGAAGAAGACAGTGAACTCAAGATTGATAAACAACAAGCCAGTGTCCCTGAAAGTATTTGCAGCTGAGAAGGAGATCGAGGAAACCCAACAAACCGATAAGGACCGATGGAGGGGACTCGCATACGATATGTCTGATGACCAACAAGACATCACCAGAGGCAAGGGTATGGTTGATTCTCTCTTCCAAGCCCCACAAGAAGCCGGAACCCATTACGCTGTCATGAGTTCATACGAGTACATTAGCACCGGTCTCCGCACATACTTGGACAACAACATGGATGGATTCTACATTGCCCCGGCTTTCATGGACAAACTTGTGGTTCACATCACCAAGAACTTCATGACTTTGCCTAACATCAAGGTTCCTCTCATTTTGGGTGTGTGGGGAGGCAAAGGTCAGGGAAAATCTTTCCAATGTGAGCTTGTGTTCGCCAAGATGGGAATCACCCCAATTATGATGAGTGCCGGAGAATTAGAAAGTGGAAACGCTGGAGAACCAGCAAAGCTGATCAGACAAAGGTACCGTGAGGCTGCAGATATCATCAAAAAGGGGAAAATGTGCTGCCTGTTCATCAACGATCTTGACGCGGGAGCAGGGAGAATGGGGGGAACCACCCAGTACACGGTGAACAACCAAATGGTTAACGCGACTCTGATGAACATCGCGGATAACCCCACCAATGTGCAACTCCCTGGTATGTACAACAAGGAAGAGAACCCGCGTGTGCCCATCATCGTCACGGGTAATGACTTCTCAACCCTCTATGCTCCCCTAATCCGTGACGGACGTATGGAGAAGTTCTACTGGGCTCCAACCAGAGAAGACCGTATCGGGGTCTGCACCGGTATCTTCAGAACTGATGGTGTTTCTACAGAAGATGTTACCAAGCTTGTCGACACTTTCCCAGGCCAATCCATTGATTTCTTCGGGGCGTTGAGGGCTAGAGTGTATGACGACGAAGTCAGGAAGTGGATTTCGGGCGTGGGTGTGGAACAAATTGGGAAAAAGCTTGTGAACTCGAGGGAAGGCCCACCGTCGTTTGAGCAACCCAAGATAACAATCGACAAGCTTCTGGAGTACGGAAACATGTTGGTTCAAGAACAGGAGAATGTGAAGAGAGTCCAGTTAGCTGATACCTATTTGGATTCGGCTGCACTCGGGGATGCTAACAGGGATTCCATCAGCCGAGGAGACTTCTACGGGAAAGCGGCCCAACAGGTGCAGGTTCCCGTTCCAGAAGGGTGCACGGACCCTGGTGCCGAGAACTTCGACCCAACGGCTAGGAGTGATGATGGCAGCTGCACTTATACTTTCTAAATATAGAAACTTTTAAGGAAAAGTATTGTCTAAGGATGTGAGGATGTCAAA >scaffold32 GGAAAGACATTTAGAGAGCAAGTTCTTCGCTGGTTAACTTATCATAAGATTTCTCAAGTTGATTCTATTGTTTTGACCCATGAACATGCTGATGCAGTACTTGGTCTTGATGACATCCGTGCAGTGCAACCATATAGTCCAATAAATGAAATTGAACCTACACCTATTTTCCTGAATCAACATGCGATGGAAAGCTTAAAAGTGAAATTTCCGTACTTGGTTCAAAAGAAGCTCAAGGCTGGTCAAGAAGTTAGACGTGTGGCACAACTTGATTGGAAAATAATTGAGAATGATTGTAAGAGTCCATTTGTTGCATCCGGGCTAGAAATTATACCCTTGCCGGTAATGCATGGGGAGGATTACATCTGTTTAGGTTTTTCATTTGGGAAACATAGCAAAGTAGCTTATATATCTGATATTTCTCGTTTCATAGAAGAAACAGAACTCTATATTTCTAAAAGAGGAGGTAAGCAGCTGGATCTTCTTATATTGGATACACTTTATAGGAACAATTCTCATAATACTCACTTTTGCTTCCCCCAGACACTTGAAGCCATTAAACGGTTGGAACCAAAGAGAGCATATTTGATCGGAATGACCCATGAATTTGATCACCACAAAGATAACGAGTTTCTACAGGATTGGTCCAAAAGAGAAGGAATTCCAGTTCAGCTTGCACATGATGGTTTGAGGATACCTATACATCTCTAACGGTTTTTGTCCGTATAAACAATTGCATATCTCTTGTTTCTTTCAATACAAATGAACGTATACGATTAATAATAGACCCTAAATCACACTAAAAATATGCTTACTAAAAACACATTTTGCCATGCAAACACAAATTTGCCTAGAATTGTACTCTTAATTGCTCTCTTGGGTGTTTTTAGTGATACGTCAAATTATATATTCACTCGATCGA >scaffold52 ACTCAGTATCCAAACGCCCCCTATGACATGTTCATCGAACACCCGCCAAAACCTTCTCGTCTGATTCATCTTCTCCGTCCAAAATCAATCAAAAACCCTAAAATTCATCCCCAAAATGAAGATCACAAAACGCTTCAATCGAGTCGTTAAACCCCTAAAACCCATAAATTCATCCACAAGTGATTTCAAACCTAATACCACCAAGAACAAACCAAATCTGAAGCTGAAATCGAAAACAAAACCTACAACAATCAAGCAGAAACCCCCAAATAAACACGATATTCATTCAATAGAATCCAAACCCTCGTTCTCACTCGAGAAATCCCCAATTTTGGGCCCTGAGTNGCAAAACCTACAACAATCAAACAAAAAGCCCCAACTCAACCCACTATTCACTCAACAGAATCAAAACCCTCGTTCTTACTCGAGAAATCCCCAATTTTGGGCCCTGAATTTTACCAAATTGACGCCCTTGATCTTGCGCCTCGGTTGCTTGGAAAGTACCTTAGGAGAGATGATGTNCCAGATTACAGAGGTGGAAGCATATAGATCTGATGATTCTGCTTGTCATGGTCGTGTTGGTGTTACTTCAAGAACTGCTCCACTGTTTGGACCAGGAGGGCATGCTTATGTGTATCTTTGCTACGGTCTGCATACGATGTTGAATGTTGTAGCTGACAAACAAGGAATTGGTTCAGCTGTCTTAATTCGTTCTTGCGCACCTGTCACTGGGTTGGAAACTATAAAACAGCGTCGGGGATTGGATACTGAGAAGCCCGTTCTTCTTACCGGGCCCGGAAAGGTTGGTCAAGCACTAGGGATCTCAACAGACTGGTCTAACCAAGCTCTCTTCACTCCTGGTGGTTTGGAGCTATTGGACGGTCCAGATGTGAAGGAAATAGTGGTGGGGCCACGTGTAGGGATAGATTATGCTTTGCCTGAACATGTTGGTGCGTTATGGAGGTTTGCAATTGCTGGTAGCCCTTGGATAAGTGCTCCTAAGAACACCCTACGCCCACCTTAATCTTTTACTGATCCATTACATTAATCTTGGTTGTGATTAGATGGTTCTTTTTAATCTTTTAGTAAAATTTAATGTTGTTTCTTNCTAAGAACACCCTACGCCCACCTTAATCTTTTACTGATCCATTACATTAATCTTGATTTTGATTAGATGCTTCTTTTTAATCTTCTAGTAAAATTTAATGTTGTTTCTCACTTTCTTTTGTCCGGGGTTTAATATAACATGTCACTTTATGGGTTTAAAAAGCG >scaffold53 AAAGCCTTCACAAACCCAACACACCACATGTCAAGAATTTACATGGCCAATAATACACAGACATGACTAATCTAATGTAGCATCTTGAATCTTTTGCACATTACTTCATATCTAAAAATGAAAATATAAATTTCATAACACACAGTGACAATAACGCCAAGGGCAGGATCAGTGATGAGGTACACCACTACACGGGACTCAACATTCTCATCCAAGAAAACAACTCAAACCTAGTGATAATTTAATAACTTTTAAAGTTGAGATAATCCTCCTAAAGACGTAAAAGCCTAGAATTTCTATTTCGATAAGAAGCACGGCATTGAGCATTGTGATTTCTCGCCTTGAGGTCCCAACTTAGCCCCATGACACCCCCCCCTCCTTAAACCCACAAAAAAACTCAGCTAAAAAAAACATAGAAAGATCATGGCTAAGGTTGGTGATGAGGTACAAGAACTCAACATTCCCATCCAAGAACACAACTTTGAAAATGATAATTTAGTAACTTCTAGTAGTTCAGATAACTCGAACCTCCTACTGCTACAAGACGCTTTTGGCTAGCAAACTGTAACATCGCAATACTTGTTACAATAAACTTATAATCAACATATGATCATCTGATCAGCATTTCCTTTGTTTTCCAATGATGCAAAACACATGATCAAGAATTCACATCACCACACAAACAAACAAACATGATTGATCTAATGTAGCATCTTAAATCTTCTGCACAGAACTTCATATCTAAAGTTGAAATTAGATCATACAACACATGGAGACATTAAGGCCATGGGCACAGCCAGTGATGAGGTACGCAACTACATGGAACTCATCATTCCCATCCAAGAAGACAACTCAAACCCAATGATAATTTATTAACTTCTATAAGTTGAGATAACTTGATCCTCCTAGAGCCATAAAGCCCTAATATTTCCATTTCAATAAGGAGCAAGGTATTTTGCAATGTGATTTCTTGAGCCTTGAGGTCCCAACTCAGCGTCTCAGCCCCAAAACCCAATTTCACTTATAGAACACGTTATGTCGAGAAAAATAATCCAAATGATGGCATACACATATGCTTCGATTGACAAGTAGATAAACGACATTTAATATAATTATAAGTTCAAATTAACGACGAGCCTTGCCGAAAAGAAACAATATCCAAAATAGCATATGCATATAGTAATAAATGTCTCTTATGAGATTAACATTTAAAAAAGATCTAGACTTCAATTCAGAGTACCAGATTTTTGCTTCGATAAGCACTCTAAGGGACCACAACTTAGCATGAGATAGTTTATCTATGTCCTTGAACCCGTTGCATATCATATGTGCCCCATGATCCAGGTCCAGGTCCATACTGAGGATAGCCTTCGGCACTAGGCTGCACAGGATTCCTTTGATTAGTAGAACTCATTCCATAATTTGCAGGATAAGGATTCACACCATAGTTAGCTTCAACATTTCCATAATTTGTAGTATAACCAGGATTTGGATTCCCTACTGCGGCAGCAGCACGGGCCCTTTTTTCAGCATTAGCCATCTCGGCACGTAACTTTTCCAGCTCACGAGCCATAGAGAGTAAATTCTTCTCCATCACCTGGCCATGTTCATAGTTCTCTGCAAGCCCCTTCTTCTCATGTTCAATTGCAGCCCTTGCATGTTGCAGTTCCTGCCTAAGCCCTCCAATTTCCGACTTGAGTGCTGGAACTTGCTGCAAGTCAGCATTAGCTCTAGCAAAATCTTGGGTCATAGCCTGAACTTGAGCAGTAAGCTTTTGACGTGTAGCAGTCAATTCGTTAATATCAGCATGCAAATTCATAAGCTCACCCCGCATGCCTTCAACCCCATGAAGATCACGTTCCACTTTAGCCGACTTCTCATACAGCTCCCTCATCTGCATATCCTTCTCCATCAGGAGGTTTCTAGCAAAATTATCGGTTTGTTGAAGCTCATGTTGTGCAGCTTCTAATTCCTGCTTAATCGCAACATGGGTTGCAGCTAATCGCTGATTATCAACCAATAGCCCCTGAATGTCCTGATGTTGAACTGCTAATTGCTCCTCAATGATAGCAGGGTGAGGCGGGTGTGGTCTGTGAGCCCTTGCAAACTCAGCTTCCCTCATCTCTTCAAGCAAGGCAGGGTGGGGGCCATGGGGCATTGGGCCTACATTCCTCCCAAATGGTGGAGGTCCACGATTCCTCCCAGACATCTTTCTCAGAGAAATTCAGCAAATGAAAGAACCTAAGACCTTGGAGGGCGTATTAATCTAGTATATCAGCATACCCAGAGGAGAGACAAAGATTGACGCAAGGTCAAGTTCGCCTTGCAATGGTGTTATGACTTATGAGGTGGTCGGTTTCTTCGATCCGAA >scaffold90 GAGCTCTCCTGTCAGGTTTTTATATATAATAAAATCTTTAAACGTTGTTTATGTACTTTAGATAATTCGCTAAGTCGATGCATCTATATGTTGCATTACATTGCAGATACACGAGGAGGCACGGAAGTTTTCATATCAGACAGGTGTCAAGGTGGTGGTTGTTTATGGAGGAACACCGATTAATCAACAGTTAAGNCTCTCCTGTCAGATACACGAGGAGGCACGGAAGTTTTCATATCAGACAGGTGTCAAAGTGGTGGTTGTTTATGGAGGAACACCGATTAATCAACAGTTAAGAGAGCTCGAGAGGGGAGTTGATATTCTTGTTGCCACACCAGGAAGGTTAGTTGATCTACTGGAGAGGGCAAAAGTGTCATTGCAAATGATAAGGTATCTAGCTCTTGATGAGGCGGATCGGATGCTGGATATGGGATTTGAGCCTCAAATTAGAAAAATTGTCGAGCAAACGGACATGCCTCCACCAGGTGAAAGACAAACAATGCTGTTCAGTGCCACATTTCCCAGAGAAATCCAGAGACTGGCATCTGATTTTCTTTCAAATTACATATTTCTAACGGTGGGTCGTGTCGGTTCAAGTACCGATTTAATTGTTCAAAGAGTGGAATTTGTGCAAGAAGTTGACAAAAGAAGCCATCTTATGGACCTCCTCCATGCTCAGAAGGAAAATGATTCTCATGGGAAGCAAGCTCTTACATTAGTTTTTGTTGAGACAAAGAAGGGAGCTGATTCACTTGAACATTGGCTTTATAGCAATGGGTTTCCTGCAACAACAATTCATGGTGACAGATCACAGCCTGAAAGAGAGCAAGCATTGAGATCATTCAAGAGCGGAAACACACCTATACTAGTTGCAACTGATGTGGCAGCACGTGGTCTTGATATCCCTCATGTTTCTCACGTGGTCAACTTTGACCTTCCGAACGACATTGACGACTACGTGCACCGTATAGGACGAACGGGCCGGGCTGGGAAAACGGGCTTGGCTACAGCTTTCTTTAACGAGAATAACTTGTCATTAGCAAAAGGATTAGCTGATTTAATCCAAGAAGCTAACCAAGAAGTACCTGCATGGCTTACTCGTTATGCTAGCCGGCCTTCTTATGGTGGCGGTAAGAACAGGCGGTCAGGTGGGCGGTTTGGTGGCCGTGACTTTAGAAAGGAAGGCTCATATGGTGGTGGTGGCAGTGGCTATGGTGGTGGCAGCAGATATGGTGGTGGCGG >scaffold103 GTCAAACTCAAAGTGGTTGTGTTCCACGCAAAGATAAGGTGTGAAGCATAAACCCCAAACCATTCCAGGATATTCTTCCTCGTGTTTGTTTCTTTCTTATCGGAAAACAACTCTGCTTCGATGCAGATCGGAGTCCTGATTTCATGGACCGCATCATAACATCATACCCTTGTTCTTCTTCTTCTACTCTAACACTGTCCCTCTCAAGATTTTGTTCAAATATCAAGAAACTAGGAAGAAGAAATTCCACTGGCATCTCTCTCTCTTGTTCAAACCCTCAAAACCCTAAATCTTTATGGCAGAAATACACCTCATCCATCAAGAAGTTACCCATTTTCAGACACTACGCCATGGATCCACTCAGTCGCCCCAGTTGCCTGCTGAATGGAGGGCTCGGTATGGCTCTGTTGAGCGTAACTGCAACGGCAAAGGTTCGTATTAGCCCCTTTGTTGCCACACTAGCTGCGAATCCAACTTTTGTCTCTGGGTTTTTTGCGTGGCTGATGGCACAATCTCTGAAAGTTGTGTTGCATTTTTGCTTTGAGAAGAAATTGGATTTGCGAATAATGTGTTCCTCTGGGGGGATGCCGTCTTCGCATTCATCTTTATGCACGGCTTTGACCACCTCAGTGGCAATATGCCATGGAGTGGCAGATTCTTTGTTTCCGGTGTGCTTAGGCTTTAGTTTGATTGTCATGTATGATGCCATTGGCGTCCGTCGTCATGCTGGGATGCAAGCAGAGGTTCTGAATGTGATAGTTGAGGACTTGTTCCAAGGTCACCCCATCAGTAAAAGGAAGCTCAAGGAGCTGCTCGGACACACCCCATCACAGGTGGTTGCTGGGGCTCTGCTTGGGATCCTGGTCGCTTGTTTTTGCTGTCAAGCCTGCTTCACTGCCATCTGAACTCGACTCTCCTTCCATCCACATAATATTATTGATATAGTTAGTAAATACCCACTCTCAAGTCTCAACTTCCCCAACCCAACTTCAAACCATCACTACCTACTTTTCATTGTAATTCTCATAACTGTCTTTTTTTTCTTTTGTGCTTTATGACTCTCAAGCATTGTTTTCTGGATTCTACAAATTTATTCTCAAGCATCTTGCTATATCAATCAAGTAAACCATATATAACAAACAAGTTTACTCCATAACCTCACCCTAGCTATTCACATCTCACACACTTATCTTGTAAGAAAACTCTAATTCAATAACCGATATTATTTACACATCATAACCTTTACCCTTGATGGGTACTCTCCATTCCCCTAGGTCGAGGTACATGTTGTCTTTCCATCACCACTTGCTATATTGACCTGGACCTTTTTCCTGATAGCCTAAATTTTCCCAACGACGTGCAAGTAGTGATCAATCACCAACCCCCATCCTGCATAACGACATTGTACGTGCATTCAAACTTGTTCACATAAGCTTTCTTCCTATAGCACGTTTGCATAACATGCCATACCATGTATCATTTTATTGTTGGCACAACATGTCATAATATAGA >scaffold109 CCAGATGAAGACGACGATAAGGAGGAAAAAGCATCGAAATCATCACTACACAACAACAAGGTGAAAAACTACTCGTGTGTTGATAACTGCTGTTGGTTCATCGGTTGCGTGTGCTCCGTGTGGTGGTTGTTGCTGTTTCTGTACAATGCGATGCCGGCGTCGTTCCCGCAGTTCGTGACGGAGGCGATCTCCGGACCGTTTCCGGATCCTCCAGGTGTAAAGTGTTTGAAGGAGGGGCTGAAGGTGAAGCATCCGGTGGTGTTTGTGCCCGGGATTGTGACCGGTGGACTTGAGCTGTGGGAGGGGCACCAGTGTATGGATGGATTGTTCAGGAAGAGGCTTTGGGGCGGTACGTTTGGTGAAGTTTATAAGAGGCCTTCATGCTGGGTACAACATATGTCGCTGGACAACAAAACTGGGATGGATCCACCAGGTATACGGGTCAGACCCGTAAATGGACTTGTAGCTGCTGATTACTTCGCCCCAGGATATTTTGTATGGGCTGTTTTGATCGCTAACTTGGCTCGTGTTGGGTATGAAGAGAAAAATATGTATATGGCTGCATATGACTGGAGACTCTCATTTCAAAACACGGAGGTAAGAGACCAAACATTGAGCCGGATAAAGAGCAATATAGAACTGATGGTTGCTACAAATGGTGGGAATAAGGCTGTTGTTATTCCACATTCAATGGGGGTTATTTATTTTCTGCATTTCATGAAGTGGGTCGAAGCACCAGCTCCAATGGGAGGTGGAGGTGGACCAGATTGGTGTGCTAAACACATAAAGGCTGTGATGAATATTGGTGGACCGTTTTTAGGTGTCCCAAAAGCTGTAGCCGGGCTTTTCTCTGCTGAAGCCAAAGATATTGCATCAGTCAGGGCTCTTGCACCAGGTGTGTTGGACTCGGATTTATTTCAGATTCAAACGTTACAACATATAATGAGAATGAGCCGCACATGGGATTCGACTATGTCTATGATACCAAAAGGCGGGGACACCATTTGGGGTGGTCTTGATTGGTCACCCGAAGAAGGGTATAGTCCAAGTAAGAGGAAAAATGGAAAAAATGACACTGAATCTTCCACCCAAAAGGAGTCAGCAAGTGAAGTATGTGAAGCAACAAATGCAAATTATGGAAGGATAATATCATTTGGGAGAGATGTAGCAGAGGCACTATCTTCAGAGATTGATAGGATAGAATTTAGGGGTGCTGTGAAGGGTAATAATGTTGCAAACAATACGTGTCGCGTTGTGTGGACTGAATATCATGACATGGGATTTGGTGGAATTAAGGCTGTTGCAGAATACAAGGTATATACAGCTGGCGAAATTGTTGATCTGCTCGAATTTGTTGCTCCAAAAATGATGGAACGGGGTAGTGCTCATTTTTCATATGGTATTGCTGATAATCTGGATGACCCAAAATATTCACATTACAAGTACTGGTCCAACCCATTGGAGACAAAGTAAGAATCCTTGTAGCTTTTTTTGTTATCTTTATGAATTTTGAGTTTTTGACATTTCAAGTAGTCCAATGTGAATGTGAGTAACCTTCAAGGTCTGAGTCCCTCTAGTAGAGGTCTTAGGTTTGAATATAGCTTTCACTGGTTTTTTGCTTTTAACCCTCTTTTGAAGACTACCTGCTCAATATGAGCTGCAATTTACCTGATTCATTGGTTAGTAGGGTATTGGTGGGGTTCTGTGAGCTTTCTGGTTATAGCAAGGTCACAAAAAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAAAAATAGTTAAAATATAATAATCCATGCACAGTTTTTAATTTAAAGTTATTTTTTATCTCATTATTAGCTAGTAATGATATCCATTTTCAGGTTACCAAATGCACCAGACATGG crb-blast-0.6.4/test/helper.rb0000644000175000017500000000055412577436147016115 0ustar mcrusoemcrusoerequire 'simplecov' require 'coveralls' SimpleCov.formatter = SimpleCov::Formatter::MultiFormatter[ SimpleCov::Formatter::HTMLFormatter, Coveralls::SimpleCov::Formatter ] SimpleCov.start require 'test/unit' begin; require 'turn/autorun'; rescue LoadError; end require 'shoulda-context' require 'crb-blast' Turn.config.format = :pretty Turn.config.trace = 5 crb-blast-0.6.4/lib/0000755000175000017500000000000012577436147014074 5ustar mcrusoemcrusoecrb-blast-0.6.4/lib/crb-blast/0000755000175000017500000000000012577436147015745 5ustar mcrusoemcrusoecrb-blast-0.6.4/lib/crb-blast/version.rb0000644000175000017500000000024512577436147017760 0ustar mcrusoemcrusoemodule CRB_Blast module VERSION MAJOR = 0 MINOR = 6 PATCH = 4 BUILD = nil STRING = [MAJOR, MINOR, PATCH, BUILD].compact.join('.') end end crb-blast-0.6.4/lib/crb-blast/hit.rb0000644000175000017500000000231112577436147017053 0ustar mcrusoemcrusoemodule CRB_Blast class Hit # Fields: query id, subject id, % identity, alignment length, mismatches, # gap opens, q. start, q. end, s. start, s. end, evalue, bit score attr_accessor :query, :target, :id, :alnlen, :mismatches, :gaps, :qstart, :qend, :tstart, :tend, :evalue, :bitscore, :qlen, :tlen, :qprot, :tprot def initialize(list, qprot, tprot) raise(RuntimeError, "unexpected number of columns") if list.length < 14 @query = list[0].split(/[\|\ ]/).first @target = list[1].split(/[\|\ ]/).first @id = list[2] @alnlen = list[3].to_i @mismatches = list[4].to_i @gaps = list[5].to_i @qstart = list[6].to_i @qend = list[7].to_i @tstart = list[8].to_i @tend = list[9].to_i @evalue = list[10].to_f @bitscore = list[11].to_f @qlen = list[12].to_f @tlen = list[13].to_f @qprot = qprot # bool @tprot = tprot # bool end def to_s s = "#{@query}\t#{@target}\t#{@id}\t#{@alnlen}\t#{@evalue}\t#{@bitscore}\t" s << "#{@qstart}..#{@qend}\t#{@tstart}..#{@tend}\t#{@qlen}\t#{@tlen}" return s end end endcrb-blast-0.6.4/lib/crb-blast/crb-blast.rb0000644000175000017500000004211312577436147020144 0ustar mcrusoemcrusoe#!/usr/bin/env ruby require 'bio' require 'fixwhich' require 'threach' module CRB_Blast class Bio::FastaFormat def isNucl? Bio::Sequence.guess(self.seq, 0.9, 500) == Bio::Sequence::NA end def isProt? Bio::Sequence.guess(self.seq, 0.9, 500) == Bio::Sequence::AA end end class CRB_Blast include Which attr_accessor :query_name, :target_name, :reciprocals attr_accessor :missed attr_accessor :target_is_prot, :query_is_prot attr_accessor :query_results, :target_results, :working_dir def initialize query, target, output=nil raise IOError.new("File not found #{query}") if !File.exist?(query) raise IOError.new("File not found #{target}") if !File.exist?(target) @query = File.expand_path(query) @target = File.expand_path(target) if output.nil? #@working_dir = File.expand_path(File.dirname(query)) # no trailing / @working_dir = "." else @working_dir = File.expand_path(output) mkcmd = "mkdir #{@working_dir}" if !Dir.exist?(@working_dir) puts mkcmd mkdir = Cmd.new(mkcmd) mkdir.run if !mkdir.status.success? raise RuntimeError.new("Unable to create output directory") end end end @makedb_path = which('makeblastdb') raise 'makeblastdb was not in the PATH' if @makedb_path.empty? @blastn_path = which('blastn') raise 'blastn was not in the PATH' if @blastn_path.empty? @tblastn_path = which('tblastn') raise 'tblastn was not in the PATH' if @tblastn_path.empty? @blastx_path = which('blastx') raise 'blastx was not in the PATH' if @blastx_path.empty? @blastp_path = which('blastp') raise 'blastp was not in the PATH' if @blastp_path.empty? @makedb_path = @makedb_path.first @blastn_path = @blastn_path.first @tblastn_path = @tblastn_path.first @blastx_path = @blastx_path.first @blastp_path = @blastp_path.first end # # makes a blast database from the query and the target # def makedb # only scan the first few hundred entries n = 100 # check if the query is a nucl or prot seq query_file = Bio::FastaFormat.open(@query) count_p=0 count=0 query_file.take(n).each do |entry| count_p += 1 if entry.isProt? count += 1 end if count_p > count*0.9 @query_is_prot = true else @query_is_prot = false end # check if the target is a nucl or prot seq target_file = Bio::FastaFormat.open(@target) count_p=0 count=0 target_file.take(n).each do |entry| count_p += 1 if entry.isProt? count += 1 end if count_p > count*0.9 @target_is_prot = true else @target_is_prot = false end # construct the output database names @query_name = File.basename(@query).split('.')[0..-2].join('.') @target_name = File.basename(@target).split('.')[0..-2].join('.') # check if the databases already exist in @working_dir make_query_db_cmd = "#{@makedb_path} -in #{@query}" make_query_db_cmd << " -dbtype nucl " if !@query_is_prot make_query_db_cmd << " -dbtype prot " if @query_is_prot make_query_db_cmd << " -title #{query_name} " make_query_db_cmd << " -out #{@working_dir}/#{query_name}" db_query = "#{query_name}.nsq" if !@query_is_prot db_query = "#{query_name}.psq" if @query_is_prot if !File.exists?("#{@working_dir}/#{db_query}") make_db = Cmd.new(make_query_db_cmd) make_db.run if !make_db.status.success? msg = "BLAST Error creating database:\n" + make_db.stdout + "\n" + make_db.stderr raise RuntimeError.new(msg) end end make_target_db_cmd = "#{@makedb_path} -in #{@target}" make_target_db_cmd << " -dbtype nucl " if !@target_is_prot make_target_db_cmd << " -dbtype prot " if @target_is_prot make_target_db_cmd << " -title #{target_name} " make_target_db_cmd << " -out #{@working_dir}/#{target_name}" db_target = "#{target_name}.nsq" if !@target_is_prot db_target = "#{target_name}.psq" if @target_is_prot if !File.exists?("#{@working_dir}/#{db_target}") make_db = Cmd.new(make_target_db_cmd) make_db.run if !make_db.status.success? raise RuntimeError.new("BLAST Error creating database") end end @databases = true [@query_name, @target_name] end # Construct BLAST output file name and run blast with multiple chunks or # with multiple threads # # @param [Float] evalue The evalue cutoff to use with BLAST # @param [Integer] threads The number of threads to run # @param [Boolean] split If the fasta files should be split into chunks def run_blast(evalue, threads, split) if @databases @output1 = "#{@working_dir}/#{query_name}_into_#{target_name}.1.blast" @output2 = "#{@working_dir}/#{target_name}_into_#{query_name}.2.blast" if @query_is_prot if @target_is_prot bin1 = "#{@blastp_path} " bin2 = "#{@blastp_path} " else bin1 = "#{@tblastn_path} " bin2 = "#{@blastx_path} " end else if @target_is_prot bin1 = "#{@blastx_path} " bin2 = "#{@tblastn_path} " else bin1 = "#{@blastn_path} " bin2 = "#{@blastn_path} " end end if split and threads > 1 run_blast_with_splitting evalue, threads, bin1, bin2 else run_blast_with_threads evalue, threads, bin1, bin2 end return true else return false end end # Run BLAST using its own multithreading # # @param [Float] evalue The evalue cutoff to use with BLAST # @param [Integer] threads The number of threads to run # @param [String] bin1 # @param [String] bin2 def run_blast_with_threads evalue, threads, bin1, bin2 # puts "running blast with #{threads} threads" cmd1 = "#{bin1} -query #{@query} -db #{@working_dir}/#{@target_name} " cmd1 << " -out #{@output1} -evalue #{evalue} " cmd1 << " -outfmt \"6 std qlen slen\" " cmd1 << " -max_target_seqs 50 " cmd1 << " -num_threads #{threads}" cmd2 = "#{bin2} -query #{@target} -db #{@working_dir}/#{@query_name} " cmd2 << " -out #{@output2} -evalue #{evalue} " cmd2 << " -outfmt \"6 std qlen slen\" " cmd2 << " -max_target_seqs 50 " cmd2 << " -num_threads #{threads}" if !File.exist?("#{@output1}") blast1 = Cmd.new(cmd1) blast1.run if !blast1.status.success? raise RuntimeError.new("BLAST Error:\n#{blast1.stderr}") end end if !File.exist?("#{@output2}") blast2 = Cmd.new(cmd2) blast2.run if !blast2.status.success? raise RuntimeError.new("BLAST Error:\n#{blast2.stderr}") end end end # Run BLAST by splitting the input into multiple chunks and using 1 thread # for each chunk # # @param [Float] evalue The evalue cutoff to use with BLAST # @param [Integer] threads The number of threads to run # @param [String] bin1 # @param [String] bin2 def run_blast_with_splitting evalue, threads, bin1, bin2 # puts "running blast by splitting input into #{threads} pieces" if !File.exist?(@output1) blasts=[] files = split_input(@query, threads) threads = [threads, files.length].min files.threach(threads) do |thread| cmd1 = "#{bin1} -query #{thread} -db #{@working_dir}/#{@target_name} " cmd1 << " -out #{thread}.blast -evalue #{evalue} " cmd1 << " -outfmt \"6 std qlen slen\" " if bin1=~/blastn/ cmd1 << " -dust no " elsif bin1=~/blastx/ or bin1=~/blastp/ or bin1=~/tblastn/ cmd1 << " -seg no " end cmd1 << " -soft_masking false " cmd1 << " -max_target_seqs 50 " cmd1 << " -num_threads 1" if !File.exists?("#{thread}.blast") blast1 = Cmd.new(cmd1) blast1.run if !blast1.status.success? raise RuntimeError.new("BLAST Error:\n#{blast1.stderr}") end end blasts << "#{thread}.blast" end cat_cmd = "cat " cat_cmd << blasts.join(" ") cat_cmd << " > #{@output1}" catting = Cmd.new(cat_cmd) catting.run if !catting.status.success? raise RuntimeError.new("Problem catting files:\n#{catting.stderr}") end files.each do |file| File.delete(file) if File.exist?(file) end blasts.each do |b| File.delete(b) # delete intermediate blast output files end end if !File.exist?(@output2) blasts=[] files = split_input(@target, threads) threads = [threads, files.length].min files.threach(threads) do |thread| cmd2 = "#{bin2} -query #{thread} -db #{@working_dir}/#{@query_name} " cmd2 << " -out #{thread}.blast -evalue #{evalue} " cmd2 << " -outfmt \"6 std qlen slen\" " cmd2 << " -max_target_seqs 50 " cmd2 << " -num_threads 1" if !File.exists?("#{thread}.blast") blast2 = Cmd.new(cmd2) blast2.run if !blast2.status.success? raise RuntimeError.new("BLAST Error:\n#{blast2.stderr}") end end blasts << "#{thread}.blast" end cat_cmd = "cat " cat_cmd << blasts.join(" ") cat_cmd << " > #{@output2}" catting = Cmd.new(cat_cmd) catting.run if !catting.status.success? raise RuntimeError.new("Problem catting files:\n#{catting.stderr}") end files.each do |file| File.delete(file) if File.exist?(file) end blasts.each do |b| File.delete(b) # delete intermediate blast output files end end end # Split a fasta file in pieces # # @param [String] filename # @param [Integer] pieces def split_input filename, pieces input = {} name = nil seq="" sequences=0 File.open(filename).each_line do |line| if line =~ /^>(.*)$/ sequences+=1 if name input[name]=seq seq="" end name = $1 else seq << line.chomp end end input[name]=seq # construct list of output file handles outputs=[] output_files=[] pieces = [pieces, sequences].min pieces.times do |n| outfile = File.basename("#{filename}_chunk_#{n}.fasta") outfile = "#{@working_dir}/#{outfile}" outputs[n] = File.open("#{outfile}", "w") output_files[n] = "#{outfile}" end # write sequences count=0 input.each_pair do |name, seq| outputs[count].write(">#{name}\n") outputs[count].write("#{seq}\n") count += 1 count %= pieces end outputs.each do |out| out.close end output_files end # Load the two BLAST output files and store the hits in a hash # def load_outputs if File.exist?("#{@working_dir}/reciprocal_hits.txt") # puts "reciprocal output already exists" else @query_results = Hash.new @target_results = Hash.new q_count=0 t_count=0 if !File.exists?("#{@output1}") raise RuntimeError.new("can't find #{@output1}") end if !File.exists?("#{@output2}") raise RuntimeError.new("can't find #{@output2}") end if File.exists?("#{@output1}") and File.exists?("#{@output2}") File.open("#{@output1}").each_line do |line| cols = line.chomp.split("\t") hit = Hit.new(cols, @query_is_prot, @target_is_prot) @query_results[hit.query] = [] if !@query_results.has_key?(hit.query) @query_results[hit.query] << hit q_count += 1 end File.open("#{@output2}").each_line do |line| cols = line.chomp.split("\t") hit = Hit.new(cols, @target_is_prot, @query_is_prot) @target_results[hit.query] = [] if !@target_results.has_key?(hit.query) @target_results[hit.query] << hit t_count += 1 end else raise "need to run blast first" end end [q_count, t_count] end # fills @reciprocals with strict reciprocal hits from the blast results def find_reciprocals if File.exist?("#{@working_dir}/reciprocal_hits.txt") # puts "reciprocal output already exists" else @reciprocals = Hash.new @missed = Hash.new @evalues = [] @longest = 0 hits = 0 @query_results.each_pair do |query_id, list_of_hits| list_of_hits.each_with_index do |target_hit, query_index| if @target_results.has_key?(target_hit.target) list_of_hits_2 = @target_results[target_hit.target] list_of_hits_2.each_with_index do |query_hit2, target_index| if query_index == 0 && target_index == 0 && query_id == query_hit2.target e = target_hit.evalue.to_f e = 1e-200 if e==0 e = -Math.log10(e) @reciprocals[query_id] ||= [] @reciprocals[query_id] << target_hit hits += 1 @longest = target_hit.alnlen if target_hit.alnlen > @longest @evalues << {:e => e, :length => target_hit.alnlen} elsif query_id == query_hit2.target if !@missed.key?(query_id) @missed[query_id] = [] end @missed[query_id] << target_hit end end end end end end return hits end # Learns the evalue cutoff based on the length of the sequence # Finds hits that have a lower evalue than this cutoff def find_secondaries if File.exist?("#{@working_dir}/reciprocal_hits.txt") # puts "reciprocal output already exists" else length_hash = Hash.new fitting = Hash.new @evalues.each do |h| length_hash[h[:length]] = [] if !length_hash.key?(h[:length]) length_hash[h[:length]] << h end (10..@longest).each do |centre| e = 0 count = 0 s = centre*0.1 s = s.to_i s = 5 if s < 5 (-s..s).each do |side| if length_hash.has_key?(centre+side) length_hash[centre+side].each do |point| e += point[:e] count += 1 end end end if count>0 mean = e/count fitting[centre] = mean end end hits = 0 @missed.each_pair do |id, list| list.each do |hit| l = hit.alnlen.to_i e = hit.evalue e = 1e-200 if e==0 e = -Math.log10(e) if fitting.has_key?(l) if e >= fitting[l] if !@reciprocals.key?(id) @reciprocals[id] = [] found = false @reciprocals[id].each do |existing_hit| if existing_hit.query == hit.query && existing_hit.target == hit.target found = true end end if !found @reciprocals[id] << hit hits += 1 end end end end end end end return hits end def clear_memory # running lots of jobs at the same time was keeping a lot of stuff in # memory that you might not want so this empties out those big hashes. @query_results = nil @target_results = nil end # delete blast database files def tidy_up Dir["*nin"].each do |file| File.delete(file) end Dir["*nhr"].each do |file| File.delete(file) end Dir["*nsq"].each do |file| File.delete(file) end Dir["*blast"].each do |file| File.delete(file) end end def run evalue=1e-5, threads=1, split=true makedb run_blast evalue, threads, split load_outputs find_reciprocals find_secondaries end def size hits=0 @reciprocals.each_pair do |key, list| list.each do |hit| hits += 1 end end hits end def write_output s="" unless @reciprocals.nil? @reciprocals.each_pair do |query_id, hits| hits.each do |hit| s << "#{hit}\n" end end File.open("#{@working_dir}/reciprocal_hits.txt", "w") {|f| f.write s } end end def has_reciprocal? contig return true if @reciprocals.has_key?(contig) return false end end end crb-blast-0.6.4/lib/crb-blast/cmd.rb0000644000175000017500000000035112577436147017034 0ustar mcrusoemcrusoerequire 'open3' module CRB_Blast class Cmd attr_accessor :cmd, :stdout, :stderr, :status def initialize cmd @cmd = cmd end def run @stdout, @stderr, @status = Open3.capture3 @cmd end end endcrb-blast-0.6.4/lib/crb-blast.rb0000644000175000017500000000015212577436147016270 0ustar mcrusoemcrusoerequire 'crb-blast/cmd' require 'crb-blast/hit' require 'crb-blast/crb-blast' require 'crb-blast/version' crb-blast-0.6.4/deps/0000755000175000017500000000000012577436147014261 5ustar mcrusoemcrusoecrb-blast-0.6.4/deps/deps.yaml0000644000175000017500000000116412577436147016102 0ustar mcrusoemcrusoeblastplus: binaries: - makeblastdb - blastn - tblastn - blastp - blastx - tblastx - makembindex - psiblast - rpsblast - blastdbcmd - segmasker - dustmasker - blast_formatter - windowmasker - blastdb_aliastool - deltablast - rpstblastn - blastdbcheck version: number: '2.2.29' command: 'blastx -version' url: 64bit: macosx: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.29/ncbi-blast-2.2.29+-universal-macosx.tar.gz linux: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.29/ncbi-blast-2.2.29+-x64-linux.tar.gzcrb-blast-0.6.4/crb-blast.gemspec0000644000175000017500000000224212577436147016544 0ustar mcrusoemcrusoe require File.expand_path('../lib/crb-blast/version', __FILE__) Gem::Specification.new do |gem| gem.name = 'crb-blast' gem.version = CRB_Blast::VERSION::STRING.dup gem.date = '2015-05-19' gem.summary = "Run conditional reciprocal best blast" gem.description = "See summary" gem.authors = ["Chris Boursnell", "Richard Smith-Unna"] gem.email = 'cmb211@cam.ac.uk' gem.files = `git ls-files`.split("\n") gem.executables = ["crb-blast"] gem.require_paths = %w( lib ) gem.homepage = 'https://github.com/cboursnell/crb-blast' gem.license = 'MIT' gem.add_dependency 'trollop', '~> 2.0' gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3' gem.add_dependency 'fixwhich', '~> 1.0', '>= 1.0.2' gem.add_dependency 'threach', '~> 0.2', '>= 0.2.0' gem.add_dependency 'bindeps', '~> 1.0', '>= 1.0.3' gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2' gem.add_development_dependency 'turn', '~> 0.9', '>= 0.9.7' gem.add_development_dependency 'simplecov', '~> 0.8', '>= 0.8.2' gem.add_development_dependency 'shoulda-context', '~> 1.2', '>= 1.2.1' gem.add_development_dependency 'coveralls', '~> 0.7' end crb-blast-0.6.4/build0000755000175000017500000000003312577436147014347 0ustar mcrusoemcrusoegem build crb-blast.gemspeccrb-blast-0.6.4/bin/0000755000175000017500000000000012577436147014076 5ustar mcrusoemcrusoecrb-blast-0.6.4/bin/crb-blast0000755000175000017500000000314012577436147015673 0ustar mcrusoemcrusoe#!/usr/bin/env ruby # # run crb-blast from the cli # require 'trollop' require 'crb-blast' require 'bindeps' opts = Trollop::options do version CRB_Blast::VERSION::STRING.dup banner <<-EOS CRB-Blast v#{CRB_Blast::VERSION::STRING.dup} by Chris Boursnell Conditional Reciprocal Best BLAST USAGE: crb-blast OPTIONS: EOS opt :query, "query fasta file", :required => true, :type => String opt :target, "target fasta file", :required => true, :type => String opt :evalue, "e-value cut off for BLAST. Format 1e-5", :default => 1e-5, :type => :float opt :threads, "number of threads to run BLAST with", :default => 1, :type => :int opt :output, "output file as tsv", :required => true, :type => String opt :split, "split the fasta files into chunks and run multiple blast jobs and then"+ " combine them." end Trollop::die :query, "must exist" if !File.exist?(opts[:query]) Trollop::die :target, "must exist" if !File.exist?(opts[:target]) gem_dir = Gem.loaded_specs['crb-blast'].full_gem_path gem_deps = File.join(gem_dir, 'deps', 'deps.yaml') Bindeps.require gem_deps blaster = CRB_Blast::CRB_Blast.new(opts.query, opts.target) dbs = blaster.makedb run = blaster.run_blast(opts.evalue, opts.threads, opts.split) load = blaster.load_outputs recips = blaster.find_reciprocals secondaries = blaster.find_secondaries File.open("#{opts.output}", 'w') do |out| blaster.reciprocals.each_pair do |query_id, hits| hits.each do |hit| out.write "#{hit}\n" end end end crb-blast-0.6.4/Rakefile0000644000175000017500000000016312577436147014773 0ustar mcrusoemcrusoerequire 'rake/testtask' Rake::TestTask.new do |t| t.libs << 'test' end desc "Run tests" task :default => :test crb-blast-0.6.4/README.md0000644000175000017500000000701712577436147014612 0ustar mcrusoemcrusoeCRB-BLAST ========= Conditional Reciprocal Best BLAST - high confidence ortholog assignment. ### What is Conditional Reciprocal Best BLAST? CRB-BLAST is a novel method for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation. CRB-BLAST initially performs a standard reciprocal best BLAST. It does this by performing BLAST alignments of query->target and target->query. Reciprocal best BLAST hits are those where the best match for any given query sequence in the query->target alignment is also the best hit of the match in the reverse (target->query) alignment. Reciprocal best BLAST is a very conservative way to assign orthologs. The main innovation in CRB-BLAST is to learn an appropriate e-value cutoff to apply to each pairwise alignment by taking into account the overall relatedness of the two datasets being compared. This is done by fitting a function to the distribution of alignment e-values over sequence lengths. The function provides the e-value cutoff for a sequence of given length. CRB-BLAST greatly improves the accuracy of ortholog assignment for de-novo transcriptome assembly ([Aubry et al. 2014](http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004365)). The CRB-BLAST algorithm was designed by [Steve Kelly](http://www.stevekellylab.com), and this implementation is by Chris Boursnell and Richard Smith-Unna. The original reference implementation from the paper is available for online use at http://www.stevekellylab.com/software/conditional-orthology-assignment. ### Installation To install CRB-BLAST, simply use rubygems: `gem install crb-blast` ### Prerequisites - NCBI BLAST+ (preferably the latest version) should be installed and in your PATH. - Ruby v2.0 or later. If you don't have Ruby, we suggest installing it with [RVM](http://rvm.io). `\curl -sSL https://get.rvm.io | bash -s stable --ruby` ### Usage CRB-BLAST can be run from the command-line as a standalone program, or used as a library in your own code. #### Command-line usage CRB-BLAST can be run from the command line with: ``` crb-blast ``` The options are ``` --query, -q : query fasta file in nucleotide format --target, -t : target fasta file as nucleotide or protein --evalue, -e : e-value cut off for BLAST. Format 1e-5 (default: 1.0e-05) --threads, -h : number of threads to run BLAST with (default: 1) --output, -o : output file as tsv --split, -s: split the fasta files into chunks and run multiple blast jobs and then combine them. --help, -l: Show this message ``` An example command is: ```bash crb-blast --query assembly.fa --target reference_proteins.fa --threads 8 --output annotation.tsv ``` #### Library usage To include the gem in your code just `require 'crb-blast'` A quick example: ```ruby blaster = CRB_Blast.new('test/query.fasta', 'test/target.fasta') blaster.run(1e-5, 4, true) # to run with an evalue cutoff of 1e-5 and 4 threads ``` A longer example with each step at a time: ```ruby blaster = CRB_Blast.new('test/query.fasta', 'test/target.fasta') blaster.makedb blaster.run_blast(1e-5, 6, true) blaster.load_outputs blaster.find_reciprocals blaster.find_secondaries ``` ### Getting help Please use the issue tracker if you find bugs or have trouble running CRB-BLAST. Chris Boursnell maintains this software. ### License This is adademic software - please cite us if you use it in your work. CRB-BLAST is released under the MIT license. crb-blast-0.6.4/Gemfile0000644000175000017500000000004712577436147014622 0ustar mcrusoemcrusoesource "https://rubygems.org" gemspec crb-blast-0.6.4/.gitignore0000644000175000017500000000011612577436147015314 0ustar mcrusoemcrusoe*.lock *.nhr *.nin *.nsq *.phr *.pin *.psq *.blast coverage *~ *.gem *fa *tsv