Mercurial > repos > iuc > progressivemauve
changeset 1:bca52822843e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
| author | iuc |
|---|---|
| date | Fri, 07 Sep 2018 11:30:11 -0400 |
| parents | 74093fb62bdf |
| children | bdb752f3c6bb |
| files | macros.xml progressivemauve.xml test-data/1.gff3 test-data/1.xmfa test-data/2.xmfa tool_dependencies.xml xmfa2gff3.py xmfa2gff3.xml |
| diffstat | 8 files changed, 12738 insertions(+), 5307 deletions(-) [+] |
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--- a/macros.xml Wed Aug 17 14:46:55 2016 -0400 +++ b/macros.xml Fri Sep 07 11:30:11 2018 -0400 @@ -2,14 +2,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.4.0">progressivemauve</requirement> - <requirement type="package" version="2.7">python</requirement> - <requirement type="package" version="1.65">biopython</requirement> - <requirement type="package" version="0.6.2">bcbiogff</requirement> + <requirement type="package" version="snapshot_2015_02_13">progressivemauve</requirement> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">2.4.0</token> + <token name="@WRAPPER_VERSION@">2015_02_13</token> <xml name="stdio"> <stdio> <!-- Anything other than zero is an error -->
--- a/progressivemauve.xml Wed Aug 17 14:46:55 2016 -0400 +++ b/progressivemauve.xml Fri Sep 07 11:30:11 2018 -0400 @@ -191,10 +191,10 @@ </change_format> </data> <data format="nhx" name="output_guide_tree_file" label="${tool.name} alignment of ${on_string}: Guide tree"> - <when>output_guide_tree</when> + <filter>output_guide_tree</filter> </data> <data format="tabular" name="output_backbone_file" label="${tool.name} alignment of ${on_string}: Backbone"> - <when>output_backbone</when> + <filter>output_guide_tree</filter> </data> </outputs> <tests> @@ -204,12 +204,12 @@ </test> <test> <param name="sequences" value="merged.fa" /> - <output name="output" file="1.xmfa" lines_diff="20"/> + <output name="output" file="2.xmfa" lines_diff="20"/> </test> <test> <param name="sequences" value="merged.fa" /> <param name="output_guide_tree" value="True" /> - <output name="output" file="1.xmfa" lines_diff="20"/> + <output name="output" file="2.xmfa" lines_diff="20"/> <output name="output_guide_tree_file" file="1.nhx" /> </test> <test> @@ -220,7 +220,7 @@ <test> <param name="sequences" value="merged.fa" /> <param name="match_input" value="1.mums" /> - <output name="output" file="1.xmfa" lines_diff="24"/> + <output name="output" file="2.xmfa" lines_diff="24"/> </test> </tests> <help><![CDATA[
--- a/test-data/1.gff3 Wed Aug 17 14:46:55 2016 -0400 +++ b/test-data/1.gff3 Fri Sep 07 11:30:11 2018 -0400 @@ -1,25 +1,82 @@ ##gff-version 3 ##sequence-region karma 1 1 -karma progressiveMauve match 83032 140930 . - . ID=phagey;target=phagey -karma progressiveMauve match_part 83032 83041 50.0 + . Parent=phagey -karma progressiveMauve match_part 83042 83051 60.0 + . Parent=phagey -karma progressiveMauve match_part 83060 83069 60.0 + . Parent=phagey -karma progressiveMauve match_part 83070 83079 40.0 + . Parent=phagey -karma progressiveMauve match_part 83080 83089 40.0 + . Parent=phagey -karma progressiveMauve match_part 83108 83117 40.0 + . Parent=phagey -karma progressiveMauve match_part 83125 83134 70.0 + . Parent=phagey -karma progressiveMauve match_part 83144 83153 60.0 + . Parent=phagey -karma progressiveMauve match_part 83154 83163 40.0 + . Parent=phagey -karma progressiveMauve match_part 83164 83173 70.0 + . Parent=phagey -karma progressiveMauve match_part 83196 83205 40.0 + . Parent=phagey -karma progressiveMauve match_part 83206 83215 30.0 + . Parent=phagey -karma progressiveMauve match_part 140791 140800 40.0 + . Parent=phagey -karma progressiveMauve match_part 140801 140810 20.0 + . Parent=phagey -karma progressiveMauve match_part 140811 140820 60.0 + . Parent=phagey -karma progressiveMauve match_part 140821 140830 50.0 + . Parent=phagey -karma progressiveMauve match_part 140831 140840 50.0 + . Parent=phagey -karma progressiveMauve match_part 140841 140850 60.0 + . Parent=phagey -karma progressiveMauve match_part 140851 140860 20.0 + . Parent=phagey -karma progressiveMauve match_part 140861 140870 50.0 + . Parent=phagey -karma progressiveMauve match_part 140871 140880 40.0 + . Parent=phagey -karma progressiveMauve match_part 140906 140915 80.0 + . Parent=phagey +karma progressiveMauve match 83044 149558 . - . ID=phagey;target=phagey +karma progressiveMauve match_part 83044 83053 30.0 + . Parent=phagey +karma progressiveMauve match_part 83054 83063 70.0 + . Parent=phagey +karma progressiveMauve match_part 83064 83073 30.0 + . Parent=phagey +karma progressiveMauve match_part 83074 83083 40.0 + . Parent=phagey +karma progressiveMauve match_part 83084 83093 50.0 + . Parent=phagey +karma progressiveMauve match_part 83094 83103 30.0 + . Parent=phagey +karma progressiveMauve match_part 83104 83113 10.0 + . Parent=phagey +karma progressiveMauve match_part 83114 83123 60.0 + . Parent=phagey +karma progressiveMauve match_part 83124 83133 60.0 + . Parent=phagey +karma progressiveMauve match_part 83134 83143 40.0 + . Parent=phagey +karma progressiveMauve match_part 83144 83153 40.0 + . Parent=phagey +karma progressiveMauve match_part 83154 83163 50.0 + . Parent=phagey +karma progressiveMauve match_part 83164 83173 30.0 + . Parent=phagey +karma progressiveMauve match_part 83174 83183 50.0 + . Parent=phagey +karma progressiveMauve match_part 83184 83193 30.0 + . Parent=phagey +karma progressiveMauve match_part 83203 83212 70.0 + . Parent=phagey +karma progressiveMauve match_part 83213 83222 60.0 + . Parent=phagey +karma progressiveMauve match_part 83223 83232 60.0 + . Parent=phagey +karma progressiveMauve match_part 83233 83242 20.0 + . Parent=phagey +karma progressiveMauve match_part 85518 85527 20.0 + . Parent=phagey +karma progressiveMauve match_part 85528 85537 70.0 + . Parent=phagey +karma progressiveMauve match_part 85538 85547 20.0 + . Parent=phagey +karma progressiveMauve match_part 85554 85563 30.0 + . Parent=phagey +karma progressiveMauve match_part 85564 85573 30.0 + . Parent=phagey +karma progressiveMauve match_part 85574 85583 50.0 + . Parent=phagey +karma progressiveMauve match_part 85602 85611 60.0 + . Parent=phagey +karma progressiveMauve match_part 85612 85621 10.0 + . Parent=phagey +karma progressiveMauve match_part 85622 85631 50.0 + . Parent=phagey +karma progressiveMauve match_part 85632 85641 30.0 + . Parent=phagey +karma progressiveMauve match_part 85642 85651 50.0 + . Parent=phagey +karma progressiveMauve match_part 85660 85669 50.0 + . Parent=phagey +karma progressiveMauve match_part 86170 86179 50.0 + . Parent=phagey +karma progressiveMauve match_part 86180 86189 40.0 + . Parent=phagey +karma progressiveMauve match_part 86190 86199 60.0 + . Parent=phagey +karma progressiveMauve match_part 86200 86209 20.0 + . Parent=phagey +karma progressiveMauve match_part 86210 86219 30.0 + . Parent=phagey +karma progressiveMauve match_part 86220 86229 30.0 + . Parent=phagey +karma progressiveMauve match_part 86230 86239 40.0 + . Parent=phagey +karma progressiveMauve match_part 86240 86249 20.0 + . Parent=phagey +karma progressiveMauve match_part 86250 86259 60.0 + . Parent=phagey +karma progressiveMauve match_part 86260 86269 50.0 + . Parent=phagey +karma progressiveMauve match_part 86270 86279 30.0 + . Parent=phagey +karma progressiveMauve match_part 86280 86289 30.0 + . Parent=phagey +karma progressiveMauve match_part 86298 86307 60.0 + . Parent=phagey +karma progressiveMauve match_part 86308 86317 30.0 + . Parent=phagey +karma progressiveMauve match_part 86318 86327 40.0 + . Parent=phagey +karma progressiveMauve match_part 86328 86337 60.0 + . Parent=phagey +karma progressiveMauve match_part 86338 86347 50.0 + . Parent=phagey +karma progressiveMauve match_part 86348 86357 30.0 + . Parent=phagey +karma progressiveMauve match_part 86358 86367 30.0 + . Parent=phagey +karma progressiveMauve match_part 86368 86377 70.0 + . Parent=phagey +karma progressiveMauve match_part 86378 86387 30.0 + . Parent=phagey +karma progressiveMauve match_part 86405 86414 40.0 + . Parent=phagey +karma progressiveMauve match_part 91694 91703 80.0 + . Parent=phagey +karma progressiveMauve match_part 91704 91713 30.0 + . Parent=phagey +karma progressiveMauve match_part 91714 91723 40.0 + . Parent=phagey +karma progressiveMauve match_part 91724 91733 30.0 + . Parent=phagey +karma progressiveMauve match_part 91742 91751 60.0 + . Parent=phagey +karma progressiveMauve match_part 91759 91768 50.0 + . Parent=phagey +karma progressiveMauve match_part 91778 91787 40.0 + . Parent=phagey +karma progressiveMauve match_part 91788 91797 70.0 + . Parent=phagey +karma progressiveMauve match_part 91798 91807 40.0 + . Parent=phagey +karma progressiveMauve match_part 91816 91825 50.0 + . Parent=phagey +karma progressiveMauve match_part 91830 91839 60.0 + . Parent=phagey +karma progressiveMauve match_part 91840 91849 30.0 + . Parent=phagey +karma progressiveMauve match_part 91850 91859 20.0 + . Parent=phagey +karma progressiveMauve match_part 91860 91869 50.0 + . Parent=phagey +karma progressiveMauve match_part 91870 91879 30.0 + . Parent=phagey +karma progressiveMauve match_part 91880 91889 60.0 + . Parent=phagey +karma progressiveMauve match_part 91890 91899 30.0 + . Parent=phagey +karma progressiveMauve match_part 149454 149463 60.0 + . Parent=phagey +karma progressiveMauve match_part 149464 149473 50.0 + . Parent=phagey +karma progressiveMauve match_part 149474 149483 50.0 + . Parent=phagey +karma progressiveMauve match_part 149484 149493 50.0 + . Parent=phagey +karma progressiveMauve match_part 149494 149503 20.0 + . Parent=phagey +karma progressiveMauve match_part 149504 149513 60.0 + . Parent=phagey +karma progressiveMauve match_part 149514 149523 40.0 + . Parent=phagey +karma progressiveMauve match_part 149531 149540 60.0 + . Parent=phagey +karma progressiveMauve match_part 149549 149558 70.0 + . Parent=phagey
--- a/test-data/1.xmfa Wed Aug 17 14:46:55 2016 -0400 +++ b/test-data/1.xmfa Fri Sep 07 11:30:11 2018 -0400 @@ -1,2385 +1,4539 @@ #FormatVersion Mauve1 -#Sequence1File test-data/phagey.fa +#Sequence1File dataset_1.dat #Sequence1Format FastA -#Sequence2File test-data/karma.fa +#Sequence2File dataset_2.dat #Sequence2Format FastA -#BackboneFile test-data/1.xmfa.bbcols -> 1:83031-140929 - test-data/phagey.fa -ttttctcctcttttttcttagt--gaccgagggctttttaccctcggatggtttactttcactgagtct--agatgttaa -atatttatgta---gtttaccagtgaatga-ccccattatacatcaccgccttagtgtaagacaagcctt--atttactt -ttagtca------cggaaaacgaagtagccaataccaagaccgatcattacgtggtaaaaatcattccaatatgcagctg -ctctagggaagtttaactcacctaaaatcgcccagatcatcgaaccaacaaatgaagatacaactaaccagattattagt -ttaccataactcatgcgtgttcccctcctcagtcaataataacgtatattttctttaactctttttctagttctacttcc -caggatcgtaactcacttctaagtgcgtataatgccacggttgggaggttatttcgttcttcgactaaacgtaccccctc -ctttaggcctgctatgccctgtcgtatggaacttatggagctacacacctgaatacctgttgttagcctcttttcgaaat 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-gatatcgtctagtttagcccgcttgtggaacaaatcaccgcagaagagtaataccgagtcctgttctcgggctaaatcga -ataccttctgtagggtttcgatttgtgcgcggaaacggtcattttcgtattcggcatcgggctttgcatagtcattgaat -aagtgagcatgaaaatcagaaaaggcaattagtttagtcattttgtttctcctccacttctattgttacaaacccccaag -gagtatctataccataacatggtttatacttaccaccgaagctaatgtcaaagtaattgcgatcccgtagacgtttcttt -tcttctactgcttggcaatgtttcttaacttcatcgtactcctcttgagtaacataagccgtttggagcggatttttagt -tgtctggtagatgatctcggctagctctagtacaaacttgtttactcgttttacagtgtcattctcttccggtaagctat -ataaatcatgaatacggtctagttctgcgatagctctttctctagtcatcattagctttccctccgtttatttaacaaag -tctcattcatctctttagcataatctactgttacaccatcattattctttttctttgttttaaacgacttctctaaattg -tcctgtacttcttcaatgattgccatatgttctctacgttctgcatcactacggtaaggcatcatactttgcgcactacc -tactaccttaaaaccgagcattttttcgtaagggccttccggagtgttacgaagtttatctatgtacagacgagtgaaac -cagctctaaactcttcttccgattgctgaacaacgcctacaaattctacagcgttctttttacgaaccgaaccctccatg -tgttccgcggtcttaatagcggcactgtaagctgtacggtttagctgacctgctgtccagcctagtacgttataatcctg -acagattctacgaatctcttcaaatagcttaccaccatcgtctgactcgtttcccgtagcataagggttacgcagtaggt -cagggtagtcaatgagaagaacgtctacttcaataccctgtcgaattttaatgtcagatagcaattgttctatcttagca -ggcgttacagttcggggtgaataacgagcgaagaacaagttaccaaaatgctgtcgattctgtttataaaagtcctggta -cttattaaagttttcctcgttcagggctgtcccagttaagatgttactcttattctgccgtagcatagattgttcaaatt -ttagaatcattcggttttgtgtttcctctaaggcaatgaagagaacattctttttttgcttagtatagttagtcgctaag -tttgttaatacaagtgttttacctgtaccggatagggctagaattaacccaagctcgcccttagctaaacccccactcat -taagttatccacatctgggaaccccgtaggaattgtattagcgtgtagggaagataaagcttccctttttgcttctacat -cgtctatgatattgataatttcgttttgtttacctgtgatgtctagtagctcaatttcccgccactccttgtcaaccttg -tccatcatagcctcatcgttaatactagccaaagcccgctgcatgagatcaaggcgcatatgcttctttatgtacttctc -aatgttttcgtcaataactgaatcgtcatgactatctctgatctcgtataaagaattaattacattaaaataatcttgct -gttctgtagcacttctacggagacgatccaacttctcttctgtaagtgttaggagagcttcttctgttagtacactaccg -tttgtctggtaatatcgtttaacaatgttagaaatctcctcgaataccttgtcaccatcataaatagttaatggtgtttt -tggtaaaatctcttttgaaaatgtaggtgactcaattgctttacgcaaaatctctcgtctaatcggtgaactcattcttc -ttcctccctttttacctgttacacgttagtaaatctaagatcgtcctctgtaatatcatgaattgttacatacttgctcg -gtctaccatcggagtaatttactttagccttgtacccttcgtaaggaattaaataagagaaccctactctgtccgggtca -tcctcatctttaaaaataatatcccctgtaggtaatacatagtgagtaacaaacattgtagttccattttcaaaaacctt -tatgtcgaattcgattaatttctcttcactcatttacttcatcctcctttgtaataactgtgtacagtatagcataggtt -atcccatctgtaaagaggttacaactaaattaatctagctgtaacccgttcaatacgttatcgatagaattttgttctgc -tacactaccagacataactactgtacgtttctctactgtagcagctaaatcgatctcaggttcttcttgagtctgttgac -caacaattgagacaacagtatctaggtctaacatagagaaatcatctacaggaatttcattcttcccgaatgcttcaaat -gcttcttgaacatctccaaaagataagtgaagtcctttacgctcctggataagacgtaatacttgtcttgtttctttcag -tgtacgtagctggtacaaataagtcgcacctaggtcatcctttgttttatcatcagccattggactaactaaactaccaa -gtaggcggttcttcataagtgttgcttcttcttttgtcgtagcatctcgctcgatagacgctaaggtaatttgtgtatgt -tccgatcctaaaattacatatgtaggaagtgtatagctaccttctaactggattagaccttgcgtaagaataaacttttt -caacgtgttgcgaactttatatgatacattatttttacgaagcttgtcagaaatgtcgtcgtagaagttaattagttcta -cttgtttatctctatacccgtatgttccttcaaagaattcatgaatcgaatgcttatattcaagtaacccaatcgattgg -ttagcagtgtcgtatgcgtctgcgatggcttggacaacaaaatcactagcgaatgctttaggaacaatcttaaactgttt -gcagttatcatcgatacgttctttgtagtcgcagtgctcaaggtacacgttgtatgaagtatcacttgttagtgcgttca -cgaagggtaatggtgattttttattcttaccttgcgccgtaaataccgaacgtgtgaactgcgcacttagataaacagcg -gggtcaatgttattttcttcgcaaaataagcgaaagctctcaaactgtgcccatcgagacgtaccaattactttatccaa -gcctagtacatcatagtcattagatacttcgggaactgcttccccatctttcatcacttgcacttttgcattgtggtaat -ccgtgaacagagcggcatagcgattgtatagacgagataataaatatgttttatagttacctactgggttgtctgtttgt -tgaaaccagtcccagtttggtacgccacctaatagctgtaactgaccatttaacttatcgatcttcgcttgtttctcgtc -ttgtaacagttttgcttcggccatttgtgtttttgtacgacgagggcgcttgtttgggtttggttcttgtttcttcttgg -ggatttttgtttgcagtagctcgtcaatatcgataggctcctcagaattaattaatgccttgtcagatgtagtgaactgt -ataaggtctgcgttaaaacggataacagttccaccacccttacctttacggccttttaattcgatgatttctttcgatgt -aagctctctcatgtaacgttgaactgtgcggatgtctctgcctagatcaacagccaagtctttcattcgtgtgacgaaca -cagactccttagctgtttcagctaattcagataagaagtttagtacagcgggttttaaatcaacaacggataagtttaca -tatacattttcagtcattactaattgtcctcctaaaagtttttggttaccatctactatggtctgtccttattatagcat -actttataggatagtcaatagttagagacgaaaaaagccaggagattactcccctagcatcttaaccgtaaactgctctt -ctcgaaaaatcttcatgcgttcttgagaatgtgatttcaaaattttatgtgtcatgtccaaaaagtcgaagacaagtact -tggttaccatctatcccgtttaatcggagaccccgccctatacgttgcagttgttgcctcatggatttcccagccgcaag -taagaccatacaccctatgttttttaaatctatcccctcatcgacaatagttgacgcaaccatgatgtgtagttcaccgc -gtgagaatcggtctagtgtacctgtacgatgatccgggtctgacccgccgtggataaagtctacgtccaggttcttttcc -ttgagtaatgctacgatagcgtccccgtgggcaatttcttttacgctgataagaataccgccttgttttgttgtggcata -ccattcgactagtttagcagcagtagcatttctgtattcgttctctacgatacctagcttgtacgcctctaggtagttac -cagctagctcgatattacgtggttctttaattggcactacacggatggtcggcttagaagacacaccctccttgatgagg -aagtcgttggacaccttaataacaatctggttgaatagagcctgcattcgttgccaacccatcttatcctttttgtctac -tgtaccggtcagccctacacggtattgtgcattatcgaatagggatagtgatgtaaaccaggtaatcgctttagagtggt -gtacttcatccgctatcattacacgtacagacttgacaaactcctggactgttttgtatttatcaaatttcttcttgttc -ttcttctctatgattttatcaagttcgactatgtatttgtttaactgcatctgtgccttgctatcagtgaaactctgatc -gtacgctatgtattctaaatgagtctgtacatcctgccatacctttgttgtcagtgtacagtttttgatatagttacgca -agaggtgccgtgtatttttcgtacggttaaatttcggtgctacctcttctgcaataaatttaattacccggtctttatga -gtaaacttaacatccttcttcgggtcttttaaagctgatacaagcgtaggaaccataacgaatactagctgtttattctt -aaagtccaacttcccatctccgataaacccgatgtccttcggcttaattcctaagctacctccgatactcttagctgctt -gagcaaagatttctttggaatgggtgaagaaggcaattcgctctcctcgttttaggtgtggagctagttgctgaattagt -ccagcagcggtcagggtcttaccgccgttcgtactaatgttgataacccctgtttgctcctctatgattctctttactga -atcatattggtaaggacggagggtaattggttcttctccaccggttaatacaatctcttcgtccatagcttgtactgata -ataacccaggtggacgttgttcgtcaaattcgtatgtaatacttggatcaacttcctgtagttctcttaccccttctagg -aattgaggaagtagtccagtgtggaaacgttgtagtttaaaatcgtagaagtcggtaattccatcccaatagcctgcttt -atatgctttagaatgaaatgccccgtcctctttaattcctaattttgtatgagccataccctctactttttcttgaagaa -gggtattattttgataatctatctcagtgtacatagtaccgattcttaaaatcataaattgcttgctcctcctttagcta -ataggtttagtcttagctctattataccataaagttacagactaagctaaggataacccttgtataggtgacatatttta -aagctaagggagagtaaccgttagagcatattttgagtgagttttaggtactattaaattaactactctgtattattata -tttaattatttattattataatattatataaaaagatattaataatatataaacagaaaggttaagttcataatatgtca -ggaatgattgttaatatagcaagaacccttggtacatataggttttaaatatgtcaaataaaaaaaagacaccagttaag -gtgccctcaaaagtttacatttcggtaaaaatcatatcgtcgatatatatactatctgcagtaaaccagtccaaacttac -ttccaccagataatgagaagcccatgctggtgaggtaacggtagttgcatcggtctgtacccctgtccaatctactgccg -ctgacgtaaatgtaacactagtccctgatccttggtactgcatattccggatcgtagctactccggcatcgttataggaa -attttagcgaacgcaggaacaaaagatatagtacctgtcccagctccgggctttttatagaacagacgatagtttacctt -tttcgcgtaccctactgggatagcaatacagaatttagaagcctctccactacctcctgtcttcgttacttttaagctct -tagctcctgtcttaaactgggtagtgtctagcgaaaggcttagtttagtccctgtaagtgggttcgtgatagctgcacta -tccgaagaaataaaaatctcgtccactatactggctttctcaaaaccaccgtcaattaacttattgctcttggcactaac -aaaacggggcatattaggcacattatttagtataggattgtcaattttgacgaccccttttaccacatctgcaaaatagt -cagtgttagtaataagagtacccatataaacattatcaaaccaagctcctccattgttacctgcattacagtacacgata -tagtctgatttagctgtacctcctccaacaaatgttccacctaccatactaaacgaggagccttcaccatttagctcaat -ctgtgtgctagttgttaaggtcatttctacgtgtgcaggctgtaaaacaactttccctccgttattcataacagcaactt -tttggttgtaatcaacgctagcacccataacgaaaaactctccaccgggaatatcaatttggaatgcaagatcagagtta -taatacccaccttttagttgaatattctctccgtagtttactccccctcccggtatgtaagcgcaagtcccgcaattcca -ggcatctcctcggtactcgacaaggtaggtattactgaagaatttaaccccgtacttaacgtcatggatattagcatcta -caataatatgtgctactgagttgttcgcattaggcccttcaaaatggatgcctgtattttgggttttgcctcgaccaaat -acctcaaaaccttctaatacagtatctcgttgtttgtaagggttggtattacctgtcgttgtcagacttaaaattgggac -atctgaggttcctacaaacttaattttagcttttgtacctttccattttagtttagcaatatcgagtgtagcggtgtcag -atacacagtatgtcccactagggaactttagctctaaaacattggagttgataagggcagtttgggctgctctaattgct -ggcaaatcatcatgaaatagtaaagttccactattacctgcgctactcgcagccgtttgtaaagtaattacgttagtact -tgaattaatagctgtaatctttgttgcgtaacctagagtactgcctatggtggtgtttgatcctgcgattgttacacctg -taccaccggtatcggatgaaccagagctcgctaaaccgaagttagttgcagtaataacaatttggttagtagctccgcta -atcgcccaatcgccccaattattagtagaatttctaaacttttgagcaatagaatccgcagtatcccccgctataacact -agcggaaagaacagtcggctgccccgtaacaggtacgatagtcatagtcccattagctgtagctgttcctgtaatagtat -aagttttgatatgttttactccgcctcgtatatacacatcctgccctacagagaagtcagctaaacctactgatgagaaa -cttgtggaacctgaacttattgttcccatagttgttacatccgagcccgatgctccgtacgtttttacagttattgattc -tttgatacgattgaggatgtcgctaatactgttctgtagttcagcgtctttcgcatcaagtcgagtaatatctgctgtac -ttccttttaacgcctctttaattaaatctccgatacttccttgaatttctttatcttttaggtcaaggcggtcaatgtct -ttgttaagctttaagatagtttccacaattttacctgtggcatcgcctaggttaaagtatatatcatctctgtctaaagg -tcttccagccataattatttcactccttatgtaaaaatagaggagattgctctcctctctaatataacaatctgttactt -cttattatcatctattagttgtcgtagttcctgtttaagtttagctacctcatctaactccttgttcaatagtcgctggg -aatgaaccatcgccctctctctattagttgggatgaacagtctggctttagaatgaggatcgcgcttctctaaaggcatt -atacgcccctcctagctgttttaagattttatatacctaagatactacttcttatacttcgtccttaaataccgatgtga -aacgtcttacacgaggtcttacgaatcgattctctgctcgaagttctaacttgagttttaactgtgtgttaaccgctgtt -gtagaaactttttgtgtgtacgtataacgactatactcagcggattgctttgtaaccaccgggtttgctgtgaatgtctt -ccacgttgtcccgccgtctacagagtacttaggcgtaaccgatgttgctgtaggcttagctgcgtcgaacgatactgtta -tcgtattgaaaggtgcgtctgtagagtccatgttaagcgagtagtaatcaccggcagtttctgagatgaagttaacaaat -gttaaatcttcaagtgtaagcattggtgaaatgtatcggttagacttaaacgtagctcgtagcttaaccagccctacgac -cgtacccgctgttgtctgctcgatatagttagctaatggctgccaaggtacactgtcaatggacacagagcctgcatccg -ttttcgatactgtcttaatctcccagaaacatcctgtgttattaggcgttaaatacgtagccattaacaagagcatatcc -gagttaagatcagccatagggttgaattcaatgattgcttcgtcttcaaactgagccgtgtacacagagaattttaaatc -tgattcttggtggactgtccatgtacgggcattagatgagctgaataacacgccgtttacatacggttgtgaaacaatct -tttgtgaaggagcgtctactcggttttggcctagtgtagctacccacattgtgtactggttactatctgtaatgaatact -aagcagtaactttgccctgctttacacattaacgggtcgtctaatgcaattttcgtagccgttgcacctgttgcagacgt -tttaacttccgccggtgttaggatacgttctgcgtataccgtttggttagggaatccaccttcactcattccacgtactt -gcacaattacgttgtctgtagtagacttagaagcaaagtatgcgtcaaagctagttacaacacgatcttgcgggaatacg -aacgactgtgctagtgggtcatataggtttacagtaacacgagtttttgtgataacctcctcagtcgtttttaacgtccc -ttgtgctgtgtacgtagcgatagacatattagaagcgttttgaagaactacttctcggatacctgtacgaatacctgcag -ggattgtaaacttaccagaagctttcccactagcattagaacgaatagtaccggtagttgatcctgctacggtagtgcct -gttggcgtaatcggaacacgtaacccatcgaatgttagatataagttatctgccattggctgcaggttatccgcagagaa -ggtaatgtcacgttgacgaatgaactcgatagctgtgtttcgcaccgttgttgccacatctgtaagcgttcctgtacgac -cattcttcacatcgtaagcgtaactttgtcccatatcccagtgttggtttccgtctaggtctaggttgttaattaagcct -tgtagcttcttgtcgatagaagaagatcgaccatgagcccaccatctgtccatacgaacaacttgtgtcgtttctttgtt -aactgtcactttgttctgctcaatccagttgtccgcaccaggtgaaagtttaagcgtacctagtttgttatacacagaat -aagggtttacattcatcgctgcagaagctagcggttgtgtgatctctttaatttctgtataaggtgcagtaaccaatcga -ccccaactttttgcaacagacgagttagctgagaactctgggtatctcatttgatctgcaggtgcattaacctgtaatgt -gatacttgcatcgtcgaaactcatagcaacgttagatagggttaagtccatacgggagaagtctacaaaaccgtctgcga -atacgccacgtaggtttaacgggtcatctgttacgattgctttattctctaatgcttcgattgcttggttgtattctacg -ttctctaagcgatcttttacattcactagttgtggcattgttagacgaacgacaccattgtttaccggttctgccgcatc -cgcattagggtagatatacacctcaccaatcttgagagttaatgggtcttcgtgaactggtgggttagctgctcctgctc -gccctggttgaccctctaagattgtaaattgaccgatgctgtttagcgtaactaggtctgtgcgagctaagtagtaatca -taatttaagcgaataaggcctttatctttcggttttagcccggtcataccattaaagtcaatgtatgtgtcccaaccttg -tgcatctacaatagg----------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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-----------------------------------------tgtcattgttactttataatcgacatccttttgcattaca -cgatcgtattcaaatgacatcttataggaagcacccgtagttggttctttaccgttag---ggcctgtatcccaa--tta -acatactgaatgc---cactgtcttcaa -> 2:81635-118885 + test-data/karma.fa -tcttggcgacctgttcctgagtcaggtcgagggccttccggcaggcggtgatccgctgcccgatggtctgaggatgcgca -agatcggcatccttgtggatcaaggaacgagcgcgatggggcaccatcggcttcagttcggccacggcttgcatttcgtt -ctcctccgtccgtcgggaaccgcgtcattcggtgtcgggg---------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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--------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- ----------------taacacctgacatttgcgatggttccacgccgcaacgtttccttgtcgaaattgacaaagagggg -atgtacaccctctttggcaacacatcaaggccagagatgaaaaaagttgttaacccgacttaagactcaggcgccggtcg -agccgaagccgcccgcgccccgttcggtgtcgtccaggctatcgacctcgacgaccggcacgatcaggcactgttcgagg -atgatctgggcgatgcgatcgccgggcttgatctccacggtctccccgaagaagggcgcgccgaagacgtcggcctgctt -gccgtggtgggtcaggatgaccttgacctcgccggtgtaatcctcgtccaccacgccggccaggaccccgatgcccttga -cgcccaggcccgagcgcggggcgacgcgggcgtaggttccctcgggcgcggtgatcgagaggcccgtcgacagcagggcg -cgatcgccggggttcaggcgcaccgtcttctcgccgtcgtaatagacgtccaggccggcggccttgggcgagccgcgcgt -cgggagcttggcggtttgggtcagacgcttgaccttcagaaccgggccgtcgtgctgcatcttggtcaaccccctcgcct -cctcccaggacagaaactggacgtcgcgcgtgaaacgcccgtagagcacgacgttctgatcgacgcccgagcggacgtcc -acctcgatgccggcgccccgaagggcgtcggcgagggtgtaggcctgctcagcttgcgcagccctttgatagaagacggt -agctcggccgtaaaggtgggtcggggacattattttcgggcctctggttaacgggggatgtcgaggtgatcggccagggc -gtcggcgcctccgatgaaggcttcctcctcgccgcccgcgtccagcaggaagatcatcggcgaggtgttccaggtcgggt -ggccccagttctggcggacgtcctcgaacttggcgcggcggtcctcgtcgctgggctggacggcgtcataggggatgccc -tcacgatccaggtaggccttggcccggtcgcagtgcgggcagttggccttggtgtagacccggtattccggcgcgccggc -cggcgcggtgaccgccacctcgtcgaggcgcttgaccgaccagtaacgcggcgtctcggggatcgcgcagacgccatcct -cggcgcagccgtcgtcctcgggcggcggcgtccagaccggacgctgaaggaagctgaacgcccgctcccagccggggatt -tcgcccttgccgtactccgtcgagcgctgctcgaagaagttggtgtgggtcggggcgttcatgatccagtcgagccagtc -gaacggattgtccttgacgccgtagttgggcttcaggcccagttgcagcagccggcggtcggcgatgtagcggatgtact -gcttggtgtcctcgggcgtgacgccctcgatctggagtttgcggaacttgcccgagcggcgctcggcgcggttcttcgcc -gccggcttggcctcggccatgtccggggcgatcgcgaaggcctgatcgatgaacgcgtcttcgaggtcgaccatggcgcg -gcaggcgtcatagatgcgcttcttggtctcgtcgttccaggagcgcgggtgctccttgatcaactcgtgcaggagcttga -tcatcgactccacgtgatggctctcgtcgcggatcgaccactcgacgatcgtggtcatgcccttcatgcggttgcggcgc -tggaaggacatcagcagggcgaaggacgagaaaagctgcatcccctcgccgaaggccgagaacacggcgatgtcgaccat -caggtcggcgatcgagttgccgctgtcccgattgaacatgtactcgtgcttctcgcgcatcgcctcgtagtcgaggaagg -cgcggaactcgacctcgggcaggcccagggtgtcgatcagcgtcgagtaggcgtcgatgtggttggcctcggcggcgatg -aacgcgcccagcatcatccgcacttccgggtgcgggaagcgcgggccgtacttctcgaagtagccgcgcgccacgtcgac -gtcggcctgggtgaagaaccggaagagttgcgtcagcagggacttctcgtccggcgtcagcttctcgttccagtcctgga -tgtcctggtccatgggggcttcgtgcggaagccagtgcatggcctgcatggtcttgtaggcctcataggcccaggggtag -acgaacggcttgtagtagtcgcgggacttgagcagggacatgaaggggtctcaggaaaaggagggaaggggaggatgaag -gggccgccggccccttacccctcacatgccaagcagtcggacgaggccgtcgggttgagggccagcatcgcggcctcctc -ggcggagccctcggtcacgggctcctcggcgatctcgatcttcttgcgctcgaccttggcgttggtgttctcggcccgct -tgggggtcgacgagcgcaggtagtagaaggacttgacgccggcgccctcgccccagcccaggaagtggagttccgagagg -tactcggcgtccgcgtcgtggggcacgaagacgttcagggactggccctggcagatcgacttggagcggtcgaccgcgag -ggtcacgacccagcgctggtccatttcgcgggcggtccggtagaccttcaggagatgcaggcgctcggcttccggcatgg -tcacgccgtgctcggccaggaactcgggcgtgaagtgctggatcgagccctcggccgcgacgatcgacttccagaccgcc -tcggtgtccaggcccagttcgcccaggcgcttcttcagccagcggttcttgacggcgaacgagcccgacagggtcttgtg -caggaaggtgttggccgggatcggctcgatcgacggcgaggtgcccccgcagaggatcgaggacgaggcgttgggcgcca -cggccagcttgtgggcgaaccgctcgcccgtgccttccatgtccggcgcctcgccgcgctccttgcccagcagcagggaa -gccgcgtcggcctgcttgcgcatgtggacgaacagttccaggttcagccggcgggcggcgtgactctcgaacgggatgtc -cagcatctggagcagcgagtggaagccgagcaggcccaggcccaccgaccgttcgcgcacggcgctgtaggcggcgcggt -gcatctcgtccggcgcgttgtcgatgaacacctggaggcagttgtccagcatgcgcagcaggtcttcgatgaaggtcggg -tgatcccgccactccggccacttctcggcgttgacgctggagaggcagcagacggcggtccgcatcttgccgaagatgtc -gcggcccgagcccagcatgatctccgagcagttgcccgtcagatagccgttgaagaccagacggttgcgcaggggctcgg -tcgcgcagaagacgtcggccttgtgcgcgagcgggtggacgtcggcgaccgtcgccgccaggatcgaggccaccccgatc -gcggcatcgcgcggctcgatcgcgtgggccaggacgatgccgcgatccgacaggtaggccacgtcccactcggcgagcga -gaaggcgctgaccgtgtcggtcaggcggatgcgcgggtgaaggccggactcgatggccatgaggcgcatctggcggatca -ggtcgacgtcggtcgagccgacggtcagccagcgcgcgccgtcgatctcgacccactcgccggccgcgtccagcgcgccg -gccagccacgtcaggcggcgttcgacagtccaggcgaatggcaccacgccgggattgatcacctgcgggtcaaagcgcag -ggtcgtgccgtgctcgtcgccttccaggttggtcgacagcgtcgacaggcgcttgagcacctcgccgggcagggtctcgg -gcacgaaggccgacagccggttcttgtcgtcgaagccagcgaaggtcgtccagccggcggcataggcctgctcgatcggc -ggcgtcgcgtcggccagtccctcgatcaccggcgcctgggccttggccagcacggtcccgagcttcagttcgccggcccg -aacctccacgccgtccttggtgtagaacttgtggtagggggtgcagtcgagatagtcgccgtcctcgaaccagacgcgca -ccagcgaggccttctcgtcggtggggttggtctgctggatcaggacgcggctgaattcctcgccgttccagacgtcgtgg -tattcgcccttcagggcctcgatcggcaggtggccgttgcgggtcaggatttcggtctcgccggtcacgcagaggttcga -ctggcggaccttgaggccgagcttcttctgcgcctcggggaagtggcggttggaggtgtcgatgaagtggatgtagggct -cgcccgtctgcatccgcgtctcgatcagcaggcgccacagttcgcgcgcccgctcgacgcggatcacctcgccggtcttg -ggcgaacgcagggcgaactcggtgtcgtcgcgcaccgcgatcatgaactcgtcggtgacgttgacggcgttgtgcagatt -ggtgatcttgcggttctggtcgccgccggtcggcttgcgggccgtgatgaactcgcggatttccgggtggctgatgtcca -gatagacggcgttggagccccggcgcgtgccgccttggctgacggcgagaatcaggcgatcgtccaccgccatgaacggg -atcacgccggtcgactgcgaacccttcgaggtcttctcgcccaggccgcgcagggcgccgtagtaggagccgatgccgcc -gcccatcgacgagagccagataacctcgtcatagtgctcggagatcgactcgcggctgtcctcgatcgcggtgaggaagc -aggagatcggcaggccgcgcgcggacccgccgttcgacagcaggggcgtggcgaacatgaaccagaggttcgagacatag -tcgtagagccgctggccgtgctcggcgtcatccgcgaaggccgcactcgcgcgcgcgaaggcctcctggggcgagctttc -cccaggcagcagatagcgttcacggagggtctgaagggtgaagtcgtcgagcagggcgtcgcgggtgagatcgatcttga -tttcggagggtgcgacagccatggggtctcgttctcgcgtcgaggcgcgatgcgttaaaaagccctgagaaatcagggcc -ttagattgacagcaaaggatggttaagatagcctgaggggtcccgaaagtcaagattcacgacactcgtggacccctcaa -agattccttgacagcccctcggatttactcgtcggcgaacttcattccggccgcctggaggatgtccttggtattgcagg -gctttccatccaggaggaaacagaggcgggtttcgcggacccgatcccccagcgcggcgatcgcgcgttcgaggatcgtc -atcccatcgccgaggggagcgatcagcgctccggtctcgcgcgggaggcgagggccgctgcccttcgcctccttcggggc -cttgctccgcttaccggacaacgccagccacccccaccaccgcctggaactcggccagggcttggtcgacgtcgtgcccg -gcggcgatcttcgccgagaggtccgcgacggcggtgttgacccggtcgagttcggccttgaagtagtccggggtctcctt -caggatgttgaccagcgccagggtgacgatgtcgaccaccgggatgcggatggtctccccgtcggcttcgttgaacgagg -ccagcgacaggccgatggtgaagccgctcggattgtccggcgtctcggtcagggccagaaccgattgggcgagcgcgcgc -tcttcttggacctgggtgtcttcagagggggaggtcatgggattcctgctgcatgaggagggtgatgcggttgacggcgt -cgacttcgctgatcggcccggccttcaggagggcgtcgatcgtgtcggcgatcaccccctgctggtcgagggtcatgatc -gcgagcccgtagagcagcgcctgggacgcgtggcgccggacgctcggggtggtgtggtggatgatcaggtcggcctcggc -gcgatccccgctggcgggcacgaaggccgagagcgagaattccggggccagatcgtccgggatatcgagaggggcggggg -aggacatgctcggctccggtgatgtcgtgtctcctgacgattgatgtcaggattcacgacatcggtcaacaaggttaatt -cgccgcaggggcgtcccagacggcttcgcccggcacgaacttgcggaactgctggaagccccggaaattgccctggtgcg -ccttggtcagcgcggcgcccggacgggcggcgcgggcttggtgctccagcggcgaggcatggaccggctgggaggcggcc -agcttcaggaaggtcccgacgtcacgggtgatcgaggccttggagccgtcgaagtcgcggtagctggcgcgcgcgcagcg -cgacgccgacgagacgatcaggaggcggtcgatctcggagacctcgcgcagattgacgaaggcgaagtcgatcagaccca -gattgtagtcggcctgagcccgctcgttgcgcaggaagcgcgagatcgtgtcgatgtcctcttccaggttgatgaacggc -aggtgccattcgcccggccgcagcaggcgcggggtctgggcgtacaggtccgccttgatccgtcgcgccagggtctggat -ttcgtcctgggcaccggcgtcgtcgcgcagggtcaggaagttgatccagtcggtggccgagaccacgaccgagatgtagc -cgaaccattcggtggcgcggttgacccactgcttatggatgttgaggccgccttcctcgcgcggcaggcccagcttggcg -acgccggcgcgcaccgcgtccgccatctccatccagatcgcctcggccgcctcctggtcggcgttcgacagatattcgcc -cggttgcatgcccggcttgttctcgcggaacagcggcacgtagggctcgtccagcagcatcttcttgagcgggatggccc -ggctcgacgaggcgttgcggctgaacacccgatgggtcatgaagtcggcgtggaccatgcgcggatagcgcagcagcaga -ctgtccaggcgcttgccgtcctgggtgatcgacgcggccagcggcgtcgtttgaacgaaatcgagggtcggcatggatca -gtcctgggcggcgtcgagcacgatcatggcgatcgcgttgtggagatcgtcgatcccccggtcgttggtgatggtccagt -cggggacgatcaggtccatctccagttcggaggcgtgctgggaggcggcgtccttggtgaccttgcgcgggtcctcgacg -cggatgatccggcccttcagcgcccgcacggcggcggcctcgttcaggaagcggcagtccgagcagacgacatggctgta -gccgccggccgcccgcttgaaggcctcgatccaggtgtccgactcataggagcggaacatctcggtgccgatcttctgga -ggatgtcgcgggggctcttgaaggggtagcggtccaggaccgtctccttgagcaccgggtccgacatttcgaggtcggtc -acgccataggcgatcttggcgatctcccgcagcgggtcggcgaagttgatgtggcggtagccggcggcttccaggcggcg -ggcggccgtcgtcttgccgtgcccgcgcttgccggtgatggcaatcaggtccatggggttctcctagcgaaggatggtga -gggtcttggccgcgcgggtgatgcccgtgtagagccacttgtcttcgtcggcccggaagcagccgctttcgtcgatcagg -acgacatcgtcccactgcgaaccctggctggcatggcaggtgatggcgtaggcccagtccgcgacgatcgagcttttcag -cgcccgccaagccttctgctcaggcgcggtgtagcccttgttggtgcgcgagaagtgctcctcgaacatcccctggaaca -tcgtcttgtcgtggtactcgacgccgttctcgtcgctgaacgagccctggaacgtcgcgtcgccatgggtgaactcgacc -gacttgagcgaggtcacttccgtgccgttggtcaggtccgggttgtcgcggacgttcttgcggatgatcagcggctcgtt -cttctgcggccccacgcgctcgccagggtactcgacgtagccgaattccgagcgaagctgctggttgacgttccaccggg -tcttgttgcggccgacgatgaactgcgggcggtcctcgaaatcgaagacctcctcatattcggcgcggcgcatgaccttc -accccgctgccgtagtcgcggaacggcaggtccttgccttcgcgcgccagggtcgacaggtggatgatcggattgtcctg -ggcctgccggtggatttccgacaggaagaagtccggatcattggccagcaggcccgcgtcgtcctcgaccgggggaagct -gaccaggatcgcccatggcgaagatcggcaccccgtattccatcaggtcgtcggtcatccggcgcccgaccatggacgcc -tcgtcgacgacgatcaggctcgccaactggatggcgctgtcggggttcagttggaagttgatcttgtcctcgcggtaggc -cgcgctgagttcggcctccaggcgcttgatcagcttcttttgcgtgaagatgtgctggtccttgtccggatcgccgcctt -ccatggcgcagatgtagagcgcttcgctgagcgcttcccggtggttttccaggtcggtttcgagttgtgagatcggggcc -ggcttggcgcggtagatcgccgaatggatcgtgcccgcgttggtgttggcgtagccctgggccttcagcttggtccgcat -gaccttggcggccttgcccgtcggggcgacgaaggccacggtctcgggcgcgatgccgaggctgtcgagaatgaacggca -ggatggtggacttgcccgagccggcgaagccggtcatcgtcgtcaggggttgcccgtccttgatcttttcgacaacgacc -ttgcgggccgtgtcctgttgtgcgctgagcgtagtcatcggagactttcggacgagacgagggaacccgcccggacgcgc -cgggcgggttggtcgaagagatcaggagcgcttagaagcgaccccggccgcgcgaggcgcgttcggtgcgctcctcgcct -tcgtcctcgtcgtcgcgaccccggccgcgcgtcggacgctcgtcacgctcgtcctcctcgtcgcggctgcgacgggcggg -gcgctcgtcacgctcctcgcggtcgtcgtcgcggctgcggcgagccgggcgctcgtcttcctcgtcgcgcgagcgacggg -ccggacgttcgtcctcgtcgtcacggctgcggcgggcgggacgctcttccggttcgtcgtcgcgcgcggcgcggcggctc -gaacgctcttcgcgctcctccggctcgtcatcgcggctgcggcggctcgaacgctcttcgcgctcttcgcggtcgtcgtc -acgcgaacgacgggccggacgctcgtcctcgtcgtcgcggctgcgacgcgagcgcttgtcctcgacggccttgggcttgt -cgtcgtagtcgtccggcgtgccttccagcagcgcggccagttccgtctccggcatccagcgcacgatcttgaacttcggc -gcgtacttggtgaccttccggccgcccttggtcttgccctcgaaggggttggagtccagggcgatgatcggcacctcgcc -ggggtggttgcggaagctgttgccgaagtccttcaggaacgcggccagcgcccggcgcttggagacgttgttggcctgga -agaccatctcgacgtagggctcgtcgatcagacggaaatcgatcgtgtactgctcgaccgggccgtcttcctcgccgtag -ggaccgtggtccggcaggctgttcttcgacggctgcgggccgtcttgcagggcgaccatttcttcgtagacgaccttgcc -gtccacccagatcacccagccgcgcttgtaggagcgcaggttggcggccatttcggtgccgttcttcagcggctcgtctt -cggcgccgtaggagtacgtgccgtcgttgccgtcgaacttcatgaaggccttgccgtcgccgccgcccttgaggttgttg -gcctcgttggcgatcgcggcgtagaaatcgtcctggctggccagatagccgccggccgaacgcgtggtgagttcacccat -ttgctgatacctattttctgtggagttcctcggaggcgcgagtgcctccgaggctgttactaggactaggctgagactag -gctaggactggtggaagacttcgtaagttgagctactcctcgtccgccttctgagcacccttttcagagatgttcaggcg -accgtggccctcgccttccctcatgtagtcttcgatgttgagaccattttccgccagcgcttcgcgaacggcgctggtgt -cgagggtcttgcgacccttgatccacgagatggaggccttgatctttccgtctgccgacttcgcgacccggactccggtg -ttgtggaaccactgcttcagagcctccgaagcagccttgtgtcccacttcggccgcctttttcgcagccgaggcgcaccg -ctcctcggccacaaggcgttcgaactcttccaggatcggcgcgggcgtcgtcttcgagttggcctcgccgctcgtggggg -tggacttcttggtcgtctgggcgcaggcgaccttgaacgggcagtaggtgcaggagctatcgatcttgccctcggccatg -acctccgacgggtccttgatggcgaagacgtcgtgcgcgcgctgcatggcgacgtcgaacaccttctggtcgaaggggac -gacgaacacctcgatgtcgtcgaagaacgaagcgtcgatgtagatgatgaccgcgtagttgggccgccaggacgaaagct -ggcgcgtcaatcccatctggacgatcgtctggcccctatggatgcttttctcctccttcaggttcacccgaggatcgatc -gacttgatctccaggttgaagcagttggaggggtgctcgacgtccttgcgcgagccgcccagggaggcgatgccgtactc -ggccagggcgtcgtcgtcggcgtagatcaccagaccgtcgggcgtggccgacaggggcgcttcgggcgagatgagggtcc -gctggttcgcgccgccccagatcaactgggcgtcgcgggtcaggttctcggtgatccacttcacgccgggctcgacgaag -tagttctcgatcaggtcgccgcgttgcagcgcgccccaggactgctcgtagtccgggtccttcggggcgccgtgcttggc -gaaccacaccttgcgcaggcacccgaacgcctccgaggcgccgaccgacttgctgcggtcgtgcttccacaccttctggt -gggcctcgacgtattcgttaaacccggatttgaagttgatcgcagccatcgcgcaccgtcacatttctctggtatcgtga -cttgggttcatccagggtcacgggcctggggcgcggcgcgctaggggcgatcgagcttgttacgcagccagatcaggaag -gcggccccgatgcagccggcggcgatccagaacaggtcggtcacgcggccttctcccgcatcttggccgcgaccatgtct -tccatggcgtagtagcagcgctgggtggcgaggacgtcggcgatggcggtgtgggcgtcctcgaacccctcgccgatcag -gtgcttgtggaggtcgatcagcttgggcttgcgatagccgccctggcgggccggcagcttcatcagcggcatgccggcca -ggatggtgtcgaacatcgccttgcccgcgaacggatcggcgtccgggcggcccaggacgcgccggacgacattggtcatg -atcttgttgtcgaacgagacatggttgtggccgacgaccacgtcagcgaccgcgacgaggtcgcagaaggcctcgatgac -cagcacctcggtgatcccgatctgctcggaaagctcggggctgatcccgtggatggcggcggccccgcccttgccgtcct -tgccgacggtccagtcttgcagcacgttcgccgggacatcgcccaggcgcaggatcatgtccaggcgctgcatctccttg -cgttccggattggccaggatcgcgcccagttggacgacgcgaggctgttcgtccagggagcgtttgctgtccggaaagcc -ggtggtttcggtgtcgtagaaaaggatcatcgggcgatctcgttcgggagtgtcttgttaaccaagttccggatgggtgt -caagattcacgacatagaaagtcacgaagcacgactcacgccctgggctttgatgatctcgtagatacgctgggccgaca -ggctgtaggcctcggccagttgcgccaccggctcgcccttggcgtagcagtcggcgatctcggcgtagaaccgcttcttg -gcctcctcccggcgcagcttggcgtcgggggcgtggcggtcgatgaagcggtagatcgcgatccggctgaccccgtagtc -cttggcgatcaagggcacgggggcgaaggcggcgtagctttcgatgatgtcggcggcgtggtcggcgagggccatggggt -tctccaggagggcgagagcgcggtcgatcaccaccgccgcgcgcttcgagggctgtttggtcaggaagccgcagcggcgg -ccggcggcgtagggcggctccagccctacgcagaggtactggtcggcggtcgggtccgcgcggtagccgccggcggcctc -aagccaccagtgggtcccgccgtcggggtcgcgcccgaccatcggccgccagccgccgtcccaaccgtccagcagatgcc -agagcgcctcggaggcgacatagcagtgcccggcggtcgggttggaagccgtgtacgcggaacgatagggctcgtgcaga -agctcgggtgtgaggctcttctggaccgcgataagggtttcgagcggcgcctgcatcagtgcgtctccgcccaggtgcgg -ccccacttgacgtcgacatcgaccggcaggcggaaatcgaaccgctcgccggcttccttcgccgcgtcgacgatgttgcg -gcggcagatttccttgatcgccggatcgtcgcgcaccgccacctgcatttcgtcgtggacccaggccaggacggcgtagt -cgccgtgccagccatggacgagcccgtcgtcttcgttgaaggtctcgaagttgacgcaccagcccttggcgatcgtggcg -ccggcgccctggagcttggtgttgagggccgagtgcttggcccgcacgaagaggtggcggccgtcgagggcgtcgacata -gccgcgcttggcctcgcgctggacggacttgaccacctgttgcagcgccgggatgcgcgtcatgatccgccgccgcattt -ccgcgcccagggccttggccttggcgacgttcatggtcagggacgggtcgacggtgcagcccagcttgtagtcctgggcg -ccgtagatcatggcgtagatgaaggtcttggcggtgtcgcgcgactccatctccatggccgcttggtggacgccgtggac -atcgccatcgagcacgatcttgccgtactgcccgttgtcgaactccgccatgaagtgggccagacagcgcagttcgatac -cggcttggtcggcgcccatcagggtccagccctcggggacgtagaagaggtcgcggcagtcccagccgtgatcgccctcg -cggcccttcatcaggaccttcttggtgaccacctcgcccttttcgttcagggtgaactcgccctcgggcgtcagcaccgg -gcggccccggatttgcttgccgtccgggccgagcagcgggatcgtcttggcctcgtccttccactgcggcggcgacttga -agacgacgcgggggacctgggcgatgttggggttggagtgcgaggcccggttggtcaccgtgcccccgacgttgacgcgg 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-tggttggagtgctcgaccccgccaacgacgcaggactcgtcctcgcgcaggaacttcacgccgttgcagttccagacgtc -gaaggcgttggtcatcacctcctcgaagatcgagaagttcttttcgccggtccggatcgaggcgtagaccgcccgctggc -aggtgaggaagaactcggcgttgaccgggtcggcgcggtagtcggccgtcttcagccatttgttgagcgccagatcgtgg -ttgctctcgaccaccgtgaccttcgagtccggggcctgccggcccaggatggtcaggaacatcgccacctcgcgtagttc -ctgctcgacgctttcggagcccttgacatagagccggaagcgatcgtgcggatcggcgatgttgtggtggttgcgcgccc -ggaagtcggagacgtcgtggacgaagatgtgctcgggccgcaggacgtcgatcatcgacggcgtcgccacgctaccccac -acccggctcccgtcggccgagcgctgctcggtcgggaagaagccgaaggtggcggccgacacctcgggatcgatctgcgc -cacgtggacgtcgccgggcgtcaggcaggccacgcgatggccctcggtgaccacgccgtccttgacgaagacgtccaggt -catagaacgagccgtcggtgtcgcccagcaggtggcggcagaagaacttgccgtcctcgtcgacctcgaccagcaccgcg -cccaactggtggtggaagctggccttgatcccggccttcttgggaacgtagttcggcttggtgaccgcgcccgtcgtcat -gatctgcttggacggggtgtgcttcatcgtcggaacgctgacgagttgcaccttggcgtgggggaagatgccccagcgct -cgcgggtgtaggagtggaagcccgacagcgggttctcggccgtggggagggtgttcatctcgccgcagaagtcgatccgg 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-ttcctgcacgaagggcttgagcggcgtggcgatggcgccgttgccggcgaagggctcccaggcgaagaacggggcgaaat -catcgcccagggcctcgatcagggcgtcgaaggccggccgaggagtcgggtaaaagtccagcggggtcctggcatatccg -gaggcgcccagcatggaggggtctttgcgaccagcatcggagagagacatggtcgtgagggatgtcatggttaacgaagg -gtgtcaagattcacgacattgactgtcgtgacgcagcacgttaatcaggaggcaacgggccgtccttctgcattagcccc -gccgccgcgccttccaggcggcacgggccgggacggtggttggtgacgagcaggccgaggcagcggcgggcgagtcgaag -gagaacccggcgagcggcggaaggcgtcgttgacgccctcggactcgacaagcacgtggtgatgccggaaatcaccgcga -tcgcgcggacgtctggacgttgctaggcgtaaggcaggcctgccgagaagtggaaacggccggggcgggcgggacttgat -ctcgtccgcctttccgcctaagcttccctcattgcaggcgcagcaccgcccttcgctaacggccccgaggggtacgcaag -ggctagaagccttgcctgggacaggactgcctctgatccaggaacgccctgggccgcgtagcgcccatgacgcgaacgcc -ggccgagaatgggcgactaggcgtgacggcggccagaggccgcagcgacattccaagctcgatagagcgatcggcgggcc -ggggcgaaagccctgtttcgagagccagggcaacccgtcataggtcctggtcgggcgacgaggcagcaagtcccgcgaac -ggagcctctgaggtggcgtcaccaagatgcagcagacgcaaaaaggccccgatcgcgagatcggggccttttcatgttgg -agcttcgggagggactcgaaccctcataggtgttcccaccagcagagatttgcaatcccgcgcctaacctctcagtccac -cgaagcacaaaaggacctcgacgcccgaaggcccgaggtccgatccgtaaccaggggagggccgtagctgtcccctgacc -ctgaacgacaggtggcgggcttggtcgtcatcccgtcaggctcgcggcgccgctcgcctgaaccgccgatatgccacgag -ggcagtgatccgcaggtccccacaaatagcaaaaaggccacgatccgcgaggaccgtggccttttcgttttccgatgggc -tgagactacacccatcagcaatcccgcttcgaggattattccccaggtgcgaccccaggtattccctcgacgtccaccag -accccttgcggtagtccagtccgagatcatcgccgccgttcttgcgcaccccgaagggattgcgggtctggcgtttgacc -catcatggcgaactactcgacagttccttccccgctgggcttgcgacccactcaccggcgctaaccggctgacgaagctc -ttcctatcgacacctcgcgggcttgcgacccttgagatgactccgttacccgaaggccggagcatttggcgacttacgtc -cgccactggaccagtctttgcgtttttcatcgaagcggggattgaacccgcgaccgacagcttaagaggctgttgcacta -ccactgtgctattcgcaaacccaccaagacgtgctggtccagttgttcccagagcttttgaccccggaaatgcaacacgc -ctcatatctttcgccttgcgggctactcgactgctcttcaggactccgtctcccccaacctttcggccaggatgcccagc -acccctcgaactgaagcaaagctcttcaccgcgaagtgtcgaaccctgcaacccaaacggttatccgtactccctagaca -cgcttgcacgggatagtccgcttgcgacggactggcggttaaagcctcggagttaccccggccccgccttgtctcccacg -gtcttcaggtctatccccttttgcaagaggcggccagcttcccagcccggacccgtcggcttcctctgtcctcttgcgag -gtcgggcggcctatgggagaccgtccctgtcaccccgtcgccggggctttcgtcagaagcgacgatgacgttctagcgac -agcccacgtcgtcgtcaacgactttttccgtctcgatgtcgaattttttcgacagtcgtggatgacgacagtgcttgaca -ttctcgtaagcccatgctaggtgtcggaaatcgttgtaattcggacaacggaactggcggcaagacaggggtgcgaatcc -cctcgcctccaccatcgacgcccggcgctgggagtacgcgactcctgggcagggagtgttaccctggcgggctgcggccc -gagccaaaggtagccgggcgtcgttgatgggggcgactagctttcgattggcgctcgggactgaaagacgcaacggtggg -tgacctccacatcggcttgccggtgatcgggtcaggcaacagtaaatgtcgccgacaatgacaacgacgtcgtggctttc -gcctcggctcgtgaagccatcgccgcctaataagcggtagaggagcccgccgggagcttggcaacagaatcccggcaacc -ccctttcgcaggcgggaacaccaacaggcgatctgtcgggcgaccgatttccgatccgtgttcccgtcttcgaaaggtgg -tcaggcctaccctcttggtgtgctatccaagggtctggccactttacagaacgcggggtagaggagtccggttgtcctcg -tctggctcataaccaggagatcgtgggttcaaatcccactcccgctcccaatgcgaacgccggctgttgagaacgacggc -gtgacaagctcggagagaacgagcactccagtccggggtatgaggccggactagcggacgccgtagcgattgcaggcgtg -acacccggagatagcgggaccggctttccgagccgcatgctcggcgcgtaagaccgcaggcctcggccatcgggcagtgt -caggggatgaggctagtcctcggctaaccacctagcggtgaagctagggcatgcggttcggaaagccgggttcgcggttc -gtccgctacgagatggagatgtcgccggttcgagtccggcaggtcccccaaaaggaggccttagctcagtcggtagagcg -ctcctatcccacctttggtacggtggctcgacaggtaaggcatcggcctcataagccgagggttcgtcccaatcctggtt -caaatccaggtcgtacctccaaatcgacgcttgaccccaggccgcaggctgctaagcttccccggtcgggatcgtcccgc -gtcctttccaaggtcaagcccccggagcttcgcttcgggggcttttcagttcttgaccacccgcaggcgccgggcctcga -tggcgcgctcctccgccgccacgcgcgagacgtcttgcaggtgcgccttggcgatcaggtcgggcgcgcccacggcccgg -aagggcaccttgacggagaggtcgacatagcgccgcaagagaggctcgaattccagaccccgcgcctgggcgatccgcga -caatgcgccggcgacgatcgccacgaccaggacgttggtcggggtctccttggtcagggtccagatgcccggtatcgatt -gtccaggatggagttcctgccgcgacacgtcatcggcggcggcgcggaagaggttctcgtaagggacgttttcgagcatg -cgacaacgatagcgatcttttgccgcctgtctaccctctactcttgatagtagtaaagccctgatttcaacacaagcgct -aaagacgtccgccgtaatagtcccgccacatcccctcccaatagtcgatgtggtagtcggtgcaatccgggcagagccgg -cgatccctgttggggtcctcgcccttgccgtcccaatggtagcaggtcatcgacgagaccatgcccaggcgccagaaggt -cccacatcgctcgcagccgcccagggcgatttgctgcatctgccggtgaccgttccatttcgccagcggccgggaccaga -ggagatcgaccaccgcgtggcggatgctcccgtactgggtgagcccgacttgcacgaccttgcgcttacccgtccgccgg -gacacaccgcccatgaaccggtaggcgtcggtgtaatagatgcgcacctttgggaggcggagcttcttcacgtgtccatg -acctttgcgatgttgtcctccttctccttggcggcctgggcgatgcgtgcgtcgagcgagccgttcgccaccaggaagaa -gcacatgattttctcggctgtctgcccgatccggcaggcgcggtcctcggcctgctcgatcagagtcggcgtccagtccc -cctcggcgaacgccacgtcgtgcgcccgcgtcatggtgaagcctacaccggcggcctggaggttgcaaacgatgacccgg -caggtctcgtcgtcctggaacttgtcgacctgaagctggcgcttgttgacgggggtcccgccatagatcatcgccggatt -gtagtccgccaacgcctcggcgagcgccctgacgacgtcggagtggtaggcgaacaggatcagcttgtcgccgccgtcga -ggaagttcttgacccaggggatgatcgccgggagcttggccatccccagttcgcggcggacggcggcgatctcctcgaag -agcaccgccacggccggcggcgcgagccccagaacggcggcggcgtagtcgagattgagcgcccgcgagttgggcttgtc 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+-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +-------------------------------------------------------------------------------- +---------gaccccggaaatgcaacacgcctcatatctttcgccttgcgggctactcgactgctcttcaggactccgtc +tcccccaacctttcggccaggatgcccagcacccctcgaactgaagcaaagctcttcaccgcgaagtgtcgaaccctgca +acccaaacggttatccgtactccctagacacgcttgcacgggatagtccgcttgcgacggactggcggttaaagcctcgg +agttaccccggccccgccttgtctcccacggtcttcaggtctatccccttttgcaagaggcggccagcttcccagcccgg +acccgtcggcttcctctgtcctcttgcgaggtcgggcggcctatgggagaccgtccctgtcaccccgtcgccggggcttt +cgtcagaagcgacgatgacgttctagcgacagcccacgtcgtcgtcaacgactttttccgtctcgatgtcgaattttttc +gacagtcgtggatgacgacagtgcttgacattctcgtaagcccatgctaggtgtcggaaatcgttgtaattcggacaacg +gaactggcggcaagacaggggtgcgaatcccctcgcctccaccatcgacgcccggcgctgggagtacgcgactcctgggc 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+gtcgagcgagccgttcgccaccaggaagaagcacatgattttctcggctgtctgcccgatccggcaggcgcggtcctcgg +cctgctcgatcagagtcggcgtccagtccccctcggcgaacgccacgtcgtgcgcccgcgtcatggtgaagcctacaccg +gcggcctggaggttgcaaacgatgacccggcaggtctcgtcgtcctggaacttgtcgacctgaagctggcgcttgttgac +gggggtcccgccatagatcatcgccggattgtagtccgccaacgcctcggcgagcgccctgacgacgtcggagtggtagg +cgaacaggatcagcttgtcgccgccgtcgaggaagttcttgacccaggggatgatcgccgggagcttggccatccccagt +tcgcggcggacggcggcgatctcctcgaagagcaccgccacggccggcggcgcgagccccagaacggcggcggcgtagtc +gagattgagcgcccgcgagttgggcttgtcgggatcgccgtcctgtcccaccgccttgtcgaagccgtagcgctgggccg +tctccaggatcgacaaacccaggcggatgtcgcgctggtcctcggtctcgttctcgccggccagcaccgtggcctcgtag +agcttcagcgcctgggaaagctcgtcctcgcgcgccacgacctcgcggatttccgggctgtcgaggaggacgatctggcg +gaacttcggcggaagctcgggtagcacctcgcgcttgttccgccgcaccatgaaggtcgagcgcagccgatagcccagtt +cctccaggttggaggccccggtgaaattgtaggcgccgtgcttgccacgcgtgttgtcgaaccagccgtcgcagtagcgg +tagccgaagtcgttgtagctcttccccaggccgtcgggatcgaaggccttgacgatcgaccacatctcgatcgggcggtt +catcatcggcgtgcccgacaggaacacgcggcgcttggcgtcgaccgggttgaaccagatgtcggccagcaccggctcgc +ggttctcggcctcggccttcttgatctcggcggcgttggcttccttgcgcttcttgcgcaccgccgccttcgagcgcgca +tccatctgctcgccgccgaggatgaagatcgtgcgcccgctgtcgggggtcttgatcgcgtgacattcgtcg--cagacc +aggaggtcccacggctgctcgtggatttccttggagaagcgttccagga-tgtcgtagttg = -> 1:1-83030 + test-data/phagey.fa +> 1:1-3291 + dataset_1.dat tggtattacaagagagaaaggaagtaatcgatatgcaacagacagcagctaagaacacacaaccagaaggtttacatctt tacatggcaattggatcgtatgagtcggccattaacaaatatgcgcacccatataatcctggttactggaataagtataa gaaactaaaacagaaaatccttcagtggcagcagcaaatcagttaatacatagaagaagggttagaggagggaaaggaaa @@ -2421,1239 +4575,359 @@ tgaaatgttacagaaagcagatgttgatccaaacatacatagtgtactcactctagactatctaacaggtatcgactcat tagacaaaggaaaccaaccaactgaagaagaatggtacgctatgggtctagtagaaggactaatcgagggagggaataac aaatgagtagtactaaaacagcaaaagcggaggaaaaacgtgttaagcacattatggactctctaaccaggtactatacc -gggaaagagaatagcttagacaatgctagtgagttgtttaaaggtctaataacagtaccagggcttattgttccagccga -tgatgtaatattcttcaaatcactagtagtacctgctatttttattcaaactaagggaagaataaacctaattgagttgc -acgagtgtgaacgtgggttaatcaacagtgtggtctataacgcagaattagttaacaaatttcttaaacgttataaaact -aaggaggagactaaaatgaaagaacttgaagggtttgagatactaccaacaatcgaggaagacagcagtgaagagtataa -acctctattagaggtgctacctgaactaaaagaaggggatgtacttgaggtaccttctaatacaatgaatattactgttg -ttaatacacagctggtgtggcaagatatagccggtgagttaggtagtcccgtagactttaatctacctagactaaaaaca -cctgtacgtatacaacctaaatatgtaggctggcgagaagcacttgaagcatacgaggacggctaccgaattgaatgcaa -atacaatggaaagatggtatggtttaaacgagatattgctagctttgaagagcgacctttcctcgaagataaagggcttg -taggcttactagcaacaaaatgggtcgttaagtaaactgtatgtacattatagttacaccaaacaaagggggagagcaac -atggagaaattcttttcattcttagcagtagttagtgtgctaggtgcagcaggatcgggagggatgttaatctattctat -aatgaataagaataagataaagaaacctcttattatcctagcttcttgcttagtcatatgcttcttatccgcttcagtag -ttggttacaacaccgtcgtaaattctgtagcagatagagactataaggagcctagtagctcaccagaacatgaatcgaaa -tacgtggagggtatcggtaccttaaccgtagtaaaggatatctacccggaggagaccattactcttaatcaaatgagcgc -cactgtaaatgctattaagatattccgcgtagacgatccagaaggatcatttaaagcagacatcgaacgatataaaggag -aaccagtcggggacactttctactatatgacaattaacttcacaggcgataactcctccctaatgaacttagaatggtat -ggcttagcttctatatctcttgatgatggtacatggttaaatcaagaagacgatgatcttcttaacggtcaagatgaaaa -cggaaatgatattacaccagattattatggagagacttctaaagaatacacgcacatgtatgtaatcgatagcccggatg -taaatgctgttgaattagaattcgatgcagtaactggggctagctccggagtagagagcgcaccggccacaacagaaact -tactatttcgattaaaaaagttgttgactgattatcaatggcaatgtatactaaagcagtactaacaaagacccctagga -agttgctaccagcctcgaggtaaaagtaatggtaacttaaccctaacatcaggtagtagctccctagctcatatagataa -aacacatacacctagggaggaacacaacatgaaaaaattattaatgagtttagtaggaacgtcagtattggtattcggat -tagcagcgtgcagcgaggtagatacaacagaggatacaacagatacaaaagcagcagagacaacaaaagaagaaaaggtt -agtagctcaccagctcctgcagagaaaaaagaagaggctaaagcagaaccgttagcaccagttgatcttggccctggtaa -gtttaaagtaggcgatgacattaaaccaggccgctacgtagtaagcacacaatcacaatcaggtaacttcatggtatatg -gcacacttggtctagcagaagtaaatgagattctaggaactgatgagagcttcgcagtaaacaatgtaactgttacacta -gaagaaggccaggaagtagagattgctagcttaaactccgtacacttcgaacctaagaactaatgatataataaactaat -accaacccgttatccggtgctatagtagctcaccaggtagcgggtttatttatgtagtagctcaccagaaagaaggcgaa -aacgtaagtagctcactgcaccataaccgggcgggcagctggcaggattgagagccgggccgggaatgtttttttttcta -tatataagaagaaactaggatttttaaataaattaggtaaaacatgtattttcttgttgactctgcaatagaatggatgt -atagttaggatataccaaacagggaggcgttaacatgctatcaaattttgaaaaaggttttgcattatacttagaagcag -aaaaagaaatgagaaagtcacagcgtactagaaagtttaatgaaagtatttgcttaatggctagtgaagacatggagcta -atgagaaaaattgttgttggacagtgggccattaatgccgctctttctagtccatttgctagcagatacggattataaaa -aaaagttttagaatgttgttgactttaagtatacagtaatggtaagatgaatatagttaaacaaaacaaaccgaaaaggg -gaaatgaaaaatgtataaaacaactaccgatcttctaaatgcttctattcaattaaaggaggccgcggaacatgtaacaa -accgcgagcaacacgcggcatggtgggatagtaaaacggaagtttacattgaaatctataacgctctagaaagtggagct -ttcactggtgaggcccacgacgaattaaagcaagcgcagtacattataagtgaagctgaaatgtttgccgcagcttatgc -attaaatgaaaagggaacaagcggagaggaggagccggaacgtttaccgctttcaacttgggaaaacattttccgtaacc -tatctgaaatggaagaagaggactattacgacggcgttatcgaatgggtagaagttacatggttagaaggtgaaccaggt -tccggcggtgaatgggttttgtgttacggtacggaattattcgaagacggttttacaagtgaggaggaagcacaacaaag -attaactgagttagagagaatttttccacagtatattaactaaaaaaagttgtgaaatattgttgacttacagtaaataa -ggtgctaaaatgaagatagttagtaaagcaagacaaaaaaaaacttaaaccgaaaaggggaaattaaaatgaaaaatgta -actgttaaacaaatggaattaagagaatatgatttaatcgggattttagctgatgaggttgacgctgttgaaagcttatt -aaatgattatgatggaactacttatgtatgtgacgctatcagcgagattgcagataactacattcctttatataataacg -atgtttgggaaaacgcggccaacattcgagactatatcgaggaagcagttcaaaatggccttgtcgatacatctaatttt -gatcttgttaaaacgttccaagccggttactatgagtactataaccaaagtctatacgctaacattgaacatgtattatt -caactatgttgccaatttagtgaatgagttcttagaagggttaacaccggagcaatcagaacaaattgacctggacgaat -tagaaatgagaattaatggtaacttagatgagtatgacaataacagttatttctcagacttagaggactacgccgctgaa -attgtagaagaactagaggaagagttagcaacagaagaataaaaacattatagagtaggattaaactagaatttagttct -actctatatagtccttacatacaatataaggaggtaagcagatgaaaacacttattagtttgtttgatcttgaattaact 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+aagtttaaggtagacttcggtgagttagacgggcttactaaaatggaagatactacagacttaagtgatccacatattaa +aatagatatgaacggcatcagctttaaagacaaggatggtaactggactgatccgacaaaaccattcgctaactttgaaa +atatcacaattaaccactcaaatggtaaaactataaaaggcgggaaaggggttctgaaaccgatgggattattcgatgat +tttatggaggctattgaagcagaagagacaggaagaccaatcgtaaagcatttgctagtttggagtgttgatgagctact +agaccttcacaacgattacaagcagctgtacgatctatttaaggacgaggagtacttgctatatatgaaggacgtactaa +aagttataaaagcaaaaacaaattagtagtcattctttatagactgcacgcatagtataaactataacaagaagggagga +attacagtgaatgcggaagataaacgaattctaatgaaaatagtaggaagtatagccgggatgtttataatgggatacct +attcggtttcctaggggttattattagtttagtagctatttactttgtgtttaagaatgataatggtaagcaggtaggag +aagacccggagagtgaagctaaggccgcctttatctggttctgtgtgatgctagtgttagggatcgtgcttgcgtatcta +ttcggtatcattggagtaattatcggtttagggttaatcgcaggagccatctataatataatgttcgggtaaataaagaa +ttttttttaaatagttgttgactttaaagaaacatggtgctagaattagcttatcaaccaaaggaggtaacaaagtgaga +ataacacatgaacagaagatggaaattctcgaagagtggaaccttataggagagaacgattgtagaacggctctacctca +cttaacagagctacttactaaaatacttgatagtgtttctgatcctgaaaagataaactgtgggtgttatgtgtggagtg +aaaaactacaagagcatgttgaacctaatccactctgtaagaaatgcggcgggatgggttggtattacaagagagaaagg +aagtaatcgatatgcaacagacagcagctaagaacacacaaccagaaggtttacatctttacatggcaattggatcgtat +gagtcggccattaacaaatatgcgcacccatataatcctggttactggaataagtataagaaactaaaacagaaaatcct +tcagtggcagcagcaaa = -> 2:1-81634 + test-data/karma.fa +> 2:1-53548 + dataset_2.dat gggctctgggcgaagttttgtgggactactatgacttgcattatttcaagcgcaagcggtccgagtggaagtaccaaaga tttgctttggtttatcaacaacttgccgacgcggcctcggacacctccatcgcgtccaagtttcagacctacgatcacct gccccacctggagccgaaggtgctcaaggcccggcttgacgcgggtcacgccgacgagcgcgggcggccgattccggacc @@ -4323,1645 +5597,1441 @@ cgacatcagcaaacgctcacaagtcggggaccgagagccgtcatgtcgcaagaccacaacggctcgtcctcgggccaaga acgcatctaccagaaactggatgagcttggctccatgcacgcgcgcacccgtgaagatattgcccgcatccaggagatga tgcgagcggtcggttcgtcgcaggagcggatcgaaaagcgccaggaccatttcgagcgcgaaatctggcgtgagatggaa -gatcgcgccgcgcgcacgagcgcccaactcgacgagatcaagagccacaccaacctgcgcatcgaggagatcgaggccaa -ggtcgacacgatccgcgaggaacggatcgccgagaaggcccagtggcgcggccccgagaaggccatcgccgccctggtcg -ccgtcgccggggccatcgccgccttcgccacgatcctcactttcctgaagggacactaggacttatagtcaagcttgggt -gcctgcggccagaagtcgcgcttcttgacacccgatctgggccggcataaccatagggccatcgttcctgggtggagttt -tccctaatggctgtcgcgcttactgtcgtctcggttgagaccgaatctaccatccaaggtgttgaccccgacgcggcgca -tgtccgcctgatcgaggtcctgcataccgccgcagaagcgggtcttggggaaatgacgttggaagtcaaagcggagatcg -cggcgctgctccagcaggcgtccgtggaactctcccactgccggccggtgtaggggtcccgtaaatcgccatcccagagg -gagcgacgtgtccgagtctgctgagttcaacccgctcgaccaaaatcagttccctcctcgcctcaccaaggctgctgcgc -gacaggcgcggcgccaggagcgcagccagaaaaaggaccccacggccaacaagccgaactacaaggcgctcgaagccaag -accgaacgccaacggcgctatatccaggccctcaaggcgggtgaaagcgtcatcgccattggcggggccggcacggggaa -gacctacatcccgtcccggctcttcgccaagaagctgatcgaggcgaagatcgaacgcctgatcatcgcccgcgtcaccg -cctcgcgtcccaagcacgccctgggcttcctgcccggcaagctggaagccaagctcgccccgtggctcgtcccggtcatc 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-aagaccggggctgatctggccaatggcggcaccgcctcggcctcctcgacggccgaagggtcgccggatggggcttttga -caacaccgtgggtgcggcgtggttctcctcgacggcggcggatggccagtggatcaagtaccacttcaccgcgccggtcg -acgtgcgctacctgaccctgaagggctcgcagtcgcggcctaacggctcgccctcggccttttccgtccagtacagcgac -gacgactcggcctggaccaccgcctgggaagtcacgggccagacgggctgggcggcgggccagacccgcgagttccacgc -cccgatcgatctcttcttcaccgacctcgccgacgcgccgcccagctacatcgggcaggcgggcaaggccctgcgcgtca -acaccggcgagaccgccctggagttcttcacgcccgccacgaccctggcgaccatgggcgacgtcgacttcaccttcccg -ccgaccgatgggcaggtcctggccttcgacaacgcgacgggcaagtggaagccctacaccctgacgtccgaggcccagca -gccggccttccggggggaatggtccggctcgggcgagaacgtcaccctgaccttcgattccctgaccattccaagcgagt -tgacgcccgacgccaccggttggacgatcgtggggcaggccgacgctacggccggcaccacccaggccctgaaaacgcgc -ccgatcagccacaacgggctctgctatatccagcagaccgtcaactttgtcggcgatacgccgttcaaggtgcgctacaa -ggtttcctctgaatcggtggacctgttccgcgttctggtggatggctcgcaggtctactccgacggcgggaacaacggga -ccttcgaagagttctcgacgaccctgtcgggcacgcacaccatccgttatcagtacaccaaggaccctagcgcttccatc -ggcgatgactgtgtctatatcagccagatcagctacaagaaggttctggacacgccgttcatctacggtgacaccgtcac -ctatcttggcgagacctatttctgtctgaccagcaacaccaccgagacgccgggcacggggaacgactgggtcaaatacg -gcggctcgggctcgggcaccttcctgggtctcaccgacaccccggccagctattcgggacagtcgctcaaggccgtgcgg -gtcaaggccgacgagacgggcctggagttctacaccgccgcgaccggcggcagcggcggtgcgggcggcgtcctgcccga -gcgcacgcgcctgcatcgcaccaccacccaggcgatcccgtcggggacctggacggccgtccagtgggactcggaagtgg -aggacccggtcggggccttcgtgtcgagcgccaatacccgcatcaccgtcccggccggcgtccagaaggcgcgggtgacg -gcctatacgacctggaacaccagccccaccagcgcgacgattggcttggcgctgcggcgcaatggcgtcgagattggcgc -ctcgggcggcaccaacatcgccgccacccggacggggttcgccgaaagccacctgaacctcacctccgaatggttctcgg -tcacgcagggcgactactacgaggtctatgtcctccagaactccggctcctcccagtccctgaacgggccggtgtcgaag -ttcggcgagcactcctatgtccagttcgagtgggacgtgggaccggcggcccagcagtacgaagcccacgccgcccatca -gggctggcgcgtggtggtcaccgagagccagaccgacaccttcgcgacgatcgcggaattgaagttctacgaccggtccg -gaaccttggtcccgacgacgggcggcaaggtctacgacaccaactcccacgggacctatccggcctcccaggcgttcgac -ggcaacacctccacctactggtcgtcgttgcagcagacctcgaccgacctccccggcggtcccggctatatctttgcctc -gggcgtggacgtggggtcgttcaagatcaccaccaccggctcggacttcaacaccaccaactcccccaagaacttctcgc -tgcaatataccgacgacgatggggcgtcgtggaagacctacgcgatctataccaaccagacgggctggggcgtcagcgag -gagcgcaccttcaccgtgccggtggtgggcgtggcggccaacgcgccgggcggcggcaacacctcggccgactttggctc -cttcatcgccggcaagcccctggccagcgagaaagcgatccgcttcgtggtcgccaccccgttcacggtcacgaccggcg -tccaccaaggctcggccgagacggcggcgaccgcttcgcgcacgttcagcttcgccaagaatggcgttgagttcctgacc -gcgaccttcgcggcggcggggacggtggccacgttctcggccaacaccgccacgagcttcgccgccggggacatcctgct -gatcaccgccccgtcgacccaggacgccaccctggcggacatctccttcaccctcaagggaatccgatagatggccgacg -gtacggctcgcgtaacacaggagacggtggagatcatctccaccggccccaagcccgttcgcctgacccaggagacagtg -gaggtcatctcgacctcccaacgtcccacccgtttgacccaggtcaccgtggaggtgatccgatcgatcgggatcgtgac -ggaacgcccgcgccgcctcatcttcatgctcggagcctgacatggcctatattttcgtcgacggctgcgacagcggcagt -aacgccaccaacaccccgatggctcagaagtggagttgggccgtcaccaatacgagctaccttaactggggaggcacggg -gcgtttcggcggtcaggcctactatggcgccatctcctcgctcaacatctatggcgccgggaagtctttcccgatcaccg -ggacggcggtcggcaccgatgagttcttcatggggtgtagcctctacatggccggcaccgccagcggtggctacatcatg -acgttccagaactcgtcgccggttctcgacgggtcggtcacctatagcgccacggctgcgcccacccaactggcgatccg -cctgaccggttcaatgactctggcgatctatcggggcgcgacgctcctggcgacgggcaccacggtgctgacggcgggcc -agtggtatcgcatcgaggcgcggatcgtgatctccaacactggggtgtttgatattcgcctgaacggcaatcccgagatc -accttctcgggcgacacctatgacaccggcgaccagggcgtgcgacagttctgcatcttgccgaccgccaacacctccac -gtcgctgcgtttcgacgacatcgtgctctacaacagcgcggcggtcgaaggcgagccgacgacgtggctgggcgatctgc -ggatcgacaccctgcggccgaccgccaacggcgatgtcgtcaactccacgccgctctcgggcgcggcctatgcggcggtc -gatgaggtggctatcgatggcgacaccacctataccgagtcgaccaatgtcggcgacaaggacctctaccagctaggcga -cctgaccgaaacgccgcagacgatccatgcggtggtcgtcaccgccgtggccaagtcgacgggtacgaccaatcgggcgc -tcaagctcaaggtcaagtcgagcgtcgagggcgacagcgccgccaagaccgtgccgctgagcgcctatgggagcctgcaa -gcgtcgttctcgcgcgacccggcgacggcggcggcctggaccgcgaccgccgtcaacggcatgcaggccggctggcaggt -cgacacctgacgaatgtcgtgaatcttgacatcggcatatttccggaccatagtcaaggccttgattttcagcacttccg -gaattccacatgcgtgtctccgacaccggcctgaagctgatccaggcctgggaaggccttggtgacgggaaccccgccac -ggtcgacctggagccctatgtctgcccggccaaggtctggacggtcggttgggggcacgccctgaagacgccgaccggtc -agatcatcgacgtcgacgtcttcggcgccgccagggccaaggtcctggcggccgaatccatgcagcgcaagtttggcaag -ggcgcgatcacccgtgatcaggccgtcgccctgctgcgcgaggatgtcacgggcttcgagcgctcggtcgacaagatgat -cggcgcggccggcgccacccaggcccagttcgacgccctggtctcgttcgccttcaactgcggttcggcaaacctccagt -cctcgaccctcctgcgcctgcacaacgccggcaagcgcgcggtgggcgatgtgtcgatgtcggcgctctgcaaggagagc -aagctctccacgccgatcggcaacatcgccgtggccttctcgcgctggaacaaggtcaacaaggtctgggcgctgggact -gttccgccgccggctgtccgaggtcctggtctatggcgggcataatcccgacgaggcggtcaaggccgcccagggcttca -agggctgctgatcatgagcctgttcggtgtcatcgccctggcctggaagttcttcctcaacccggctgtcatgggcgtcg -tcttcgcggcgatcgccgccctgacgggattgtggctgctgggcggcccggtcctgttctggaaggtggtgcgcgacgcg -cgcctctggctcgtcgtcgcctgcgcggcggtgctcttcggctacgcccatctccagaccaagctcgaaaaggccgagca -gcgcctggaggagatcgccgaccagaagcaggcccatgacgacggccaggaggtcgtcaagaacaacatcaaaaagcagg -tcaagcgcgccaagcaggcggccaagtaccaagaggttattcacgatgccccgactggcgaaaagctcgacgcgctcctc -gacgagttcgcgcgtgatcaaggcggtgctgctcccgtccctggtgatgctcagcctgaccctggcggcgtgtcaaaccg -tcccggtcgggttctcccctgacgacctctatcccaaggaactgcggacctgcgcgcccgcgccgcaggttcccccgcgc -cccgcgcccggcgcgccccgccccgaggacgtccaggccggctacgtcaaggatgaccatctcgccggcgccgactgccg -cgacaaggtcgaatcctggaacgagcgggccgtcaagtacgaggcccagtacaaggccatgaacgccggcccggtcggca -agttcttcagcaagctcaaggggaagacgcagtgacgccgccctggatcgccgcgccgctgcgggtctgcggcaacttct -ttcgctgggtccgcctgaccctggacacgctctgcgatcgccctgaccacctccagcgcctgtcgatcatcggctcgggc -atggcggccttcccgctgatcatcgggatcatcgcgatcctggtgcatttcggcctgcacgggccggacagcgccgccgc -cctggcgaccatcccgatcatcggcaacatgggctatggcgccctggcgctctacgccctctcccaggtggcgctcctgg -ggatcatcaagggcgtgcgcctttccggtcctggcggcgtcaatgtcgagatcgagaccacctcgggcgatggcgacggc -ctgtccgacacccacaccacgatcgtcgagcgcggccggcgtcacggccgcgatcacgattgtgtccccaaccctcaagc -cggctctggcgccggcgctatcacggagtagggaccatgcgcgaaggcttcatgctggaaggctatggcggtctgaagat -cggtccgggcggcggggctgacccgtacacgaccttgggcgacggcggctcggaaggctgcatcccggtcaaggacgaca -tctccggcgacagcgggaccgagatcatctccccgctcggctatggctaaccttgcgacataaggtcgcatgtcatgatc -cttgacagaacgacgatcttcgagtatggtcgcggctcttcgacggcatcccaccgtcacccatggctcgcgacccaccg -ttcgcagggagatgctcgcgaccaaggcggtagccggaacgacgctaggctgcgaagccaagcctccggaacacgcagca -gccggctggaacgctaggccgttacgtccaaacggggccaggacctgtgaggcgaaagccgaaaggccccaccacccgac -aagggttcacgcgtgatgcggaagagggacgtcagtcctgaagtgtctcaggtgcagaaggcccgccggtttcccggcgg -gcctttttctggtctggggactaggacttagtcgaccgcttccaggcgccggcgcttgggcgcgctcgccggcagggacg -gggcaagatcgccgatcttgccgaccaccttgccgaggaacacgatccgcttgggatcgacgtcgacatgatccttcagg -tcggcgctatagacccggaacgcgccgcccttggagggacgggtgacgtgcgcgacctgcatgaccttgtccaggccgta -gacgaactcgccgccggcggtgctgggctcgacgtcgcggcggaccaccgccatgtcgcccggcttgaggccaggggcga -agtcgtggatcggggccagggccagatcggtcggctcggcctcgaagcgctcgcgaagccagtcgggatcgaggttccag -gtccgggcgcgcttgaactcgccaaggcggcctttgaaggtcacttcctcgaccgggttgggcgcgccgaccccgaaggt -gatgtattcgggcgtcgtcttcaggacgtgggcgatctgctccagcacgtcgatgtgcggcttgacgctgtcggactcgt -acatgatgtacgccgtgcgcgccagcggccggcgctcgcccgcctgcttcggctcccagcccggtttggtgctggagtcc -ttgcgggaattgctctgctgggtcaggaagatca +gatcgcgccgcgcgcacgagcgcccaac = -> 2:118886-221828 + test-data/karma.fa -cgttccgaaggtgttcagcgatccgacgcccgaggaggtcgaggacgccgtgaagctcctgaccgacgaggtcctgatcg -acttcccgttcctggactacgacaccgccggcaacgagcggcgcgagccgtccatggccaacgccctggcgatgctgatc -accccgttcatgcgccgcatgatcgatagctgcacgccggtgttcttcgtctccaagccgacgccgggcacgggcgggac -cttcctggggatggtgccgatcatcctgttcgacggcgaggagccggccccgattcgctacacccagaacgaagaggaaa -tgcagaaggcgcttttggcttctctcatgaattcaaaggcttacctcttcttcgacgacgtcaaggagttcaacaaccgg -gtgttgctgatggcgatcacctcgcgttatattggtggtcgcgtcctcggctcctcgaagaacatcgagatgccgaacaa -ctcgatctggatcgccacgggcaacaacccgctgatctcctcggaaatggcccggcgggtggtcgacatccgcctcaacg -ccaagacctcggacatccagaagcgcacctacaagcaccctgactacgtccagtggctcaaggccaatcgcggcgagatc -gtccacgcgatcctcaccctgatcgcccattggatcaactgcggcatgccgaagttcacggcccgcaagcgcgcgtcgtt -cgaggactggtccgagaaggtgggcggcgtgctgatgtgcgccaacatcgagggcttcctggacaaccgccgctcggtcg -ccgccgacatggacgaagccgcgatcaagcaactggtccgcgactggctgctcaagtggggcgagaagacccaggtcaag -atcgccgacctgtggagctacgcctacgacatggaactcgacatcgtttcgggggccaacgacgaccagaagaaggcccg -cttcatgcgcatccttccgaccctggacggccggacgttcaagatgccgcgcggcgactgcatggtccgcgccggctccg -acgccgacggcaatgtcacctatcatctggagcgcctgagcgcgacggaggaggtcctggagactgcctgacgggggtga -gtgctccaggcccacgagaaaggccccaggatcgctcctggggccttttgagtgtctgaggctggccgactagagccaga -tgatctgaggggccttgccgcgcttcctgacgatctgcacgaggccttcggcgacgagcttgccatacaggcggtcgagc -gaggcggtcttggtccggcctttgtccccggcttgctggcgccggcgcgccttgcggttctgcgcctcccgtccgtaggt -catctcgatcccggtctggaggtcctggcgcgtcagcttgccgctggcgagggcttgatcgagcaccgccacggcctcgg -gcgggtacttctcccgcgcggccttcagataggccgccttctcctcgggcgacagggtttcgacggggtcttgttcgggg -gtcggcgcggtcatgaaaatctccaggcgcgggaatgtcacccctgatgacacacccagcacgagacgtaaagtgttgac -agacgacactcgaagccggtattgaaactcctgtacggtaagggaaaacatgatcgacgacgattcagactggcaggaag -gcgagctttcgccgccccgcgccccgatcaccaccaaggacctgacggccgccgcccagagcgtcgccggcgggcgcatg -gcggcgatgcgggcggccggagaatcccatcgacgcgatttcctgatcctgcgcgggccgctgggcgtcgtccggctctc -gttcgcgcatgttccggtcctccaggcgctttggcgtgtctgggctcgcaagcggctccagcggatcgatgatcccggcg -ccaatcttgcagagatcggagccgagatgggtttggaggtcagcgcggtccgcccggtgatcaccagcctgcacaagaac -cgactgatccgcacgcgccgcagccaccacggctggcagggcgtgcgggcgacctactacccgtcggagatcgccgtcca -ggccctgggcttggcggaggtcctcggccctggtcacgccgtccaggtggggcgtaacgcctcggcctgggcgagccgca -gccagaccgagcccggcaacctgttccaacacgccgcgctgttgcggggcggggctcatgccagggcctacgattcggag -tattcatgaaatgccgcaaaccgcgaaagacctcaaagccgccgacgtccagcccgccggggctaagggaagcgcgcagc -ctggaggtgctgaaggggcggcctccacgggtgcggtccttctgagcaaggaggccatcggccagatcggcgaagccctc -ggcggccggacccattggcaggcctcgatcgcgcgtcgggtcggcgtctccaagtcgcagatcacccgctatctcaacgg -cgatcgcacgcccaacaccgccctgggcgacatcttcatggacctgatcgtcgggaacatcgaggaactgtccgacctcc -tgagcacgcccggcctgcccgaggccgagggcgcggtggtcgccgaagcccagcgccacatccagcaagccgtgcagttg -ctgcgcgacaaaatcctgtattcctgaggtcccgcatgtccctgatcgagaagctcaacaacgacgccctggccgcccgc -aaggcggcgatgcgcaaggaagccggcggcgagcacgccgttctcctggcgacggtcgcggcggacgccgccatgatcgc -caagaacgaccgccagaaccccggccgcgacgtcacggacgaggacgtcgtcgccacgctgaagaagcacatcggcggca -tcgacaccaccctggcggaactgaccaagcgcggccggtccgaggaggagcagtcgcgcttcatcgtcgagcgccggcgc -ctggaggcctatctgccccagaccctgtcgggcggcgatctgaccgacgcgatccacgccacggccgccaagctcggcgt -cgacctgcacgtcaagagcaccaaggcgatcgtcgccgatctgcaagagcagttccctggccagattgattcttcggaag -tcgcgcgctatcttaagaacgtctgatcccagacgaaatcccagtcagaacttaaaaggccccggagcgatccggggcct -tcttctatgcgtggatcggaagtcctacgccgcttccgtctcgggaccatcctcgatccaggccgcatagaggtcctcca -ggaccttgacgcgggccgggtccatgtcggacggatcgcggatgccttcgaagaccccatggcgcggcaggtcatagtcg -ccggccagggcgtagctcatcttgatgaacttccccagcggcgggttgtcatagaactccgccttctgcttggcgttgag -ccccgaggcgaccctggcgaccttgcccggccattcggggaacaggaccaggagcccgccggcgatccccttggcgacct -tgccggccttgtgggtcgagcgcttggtgtagccgcgctcgtcgagcgtggcctcgttggtgttggccttctcctcgtag -cgtccgatgcagacaccctccaggtcggccttgtccttggccttgacgttgaacccctccaggacggtcgagcggccggg -cttgtagggcgcgtccagcgagcagaagatcagaccctcgtcgtcgttttcgagggcctcgtagaacatcgccactgcct -cctgggcgttcttgagcaggcgctgctccaggatgaccacccaggacggcagcgacaactccagggccttcagggcgtcc -agacgctcggtcttgccgcccggcgccaggaagtgctcgaagacatagtagcggatgtccggctcgccttcctgggtcat -gaccgccgaggtcgacccccggaagttcagcttgccgtcggtcaggatgccgatctcgccgtccaggccgtggggcaggg -tcgacagcagccgccgcacgtggtgattggggatgtacttcagcgaccgggtgatcccgtggccgatctcgtcggcctcc -agggtgatccagccggcctcggtgtggacgagggaggtctcgatcttgtcggggtggacgggcgacacgctggcccgcac -cccgtccttcttgaacgaggcgtagcaggggaactggatgcgggcctcgaactcctcgggacgcaccgagtcggtgtcgg -ccagggcgatccggaaccgcttgtagggcttgaaaggcttgggtttcttggtcatctcaacttcccctcgatcagtttga -ggccgggctggtcccggttcatttggtagacgatgtagcgatcgccgctgaactcgacgctgtagaccgtcatgccggcg -tcgaggcactgcatccacatgtgccgcgtccccggcccgccggggaaggccacgcagacgttggccccgctctccacgcg -catccgggtgttgcggttcttgggcgcgtcgtcgccctcgccatccaggagcggatcgaccttgtagacctcggtggcga -agccccacttctcggcccaggcgcggcagagccggtcgtagccctcggcgtcgccgtcgacccagaccatgtcgcgcggc -cagcgaagcatcgagaccagggccgacaggaccagacgcggggcctgctcgacgaccccgacccggccgccgcagaccac -cgccttgaacggatcaggcttcatcgccgaaaatctccggatcgagcacgtcttcctccatgtcgatgaacccctgtagc -ggctggcgcggctcgacgcgcctgttctccagcatgatctcgtcatgcacccgcatctgcgggatgtagtcgtactcgaa -gcgccgctgccggcgtccgagcgcgtcgaggctcagatggctcccgtgatggcgctgggcgtcggacaggaattcctgat -aggcggtccgcgtcgaggcggcatgggtggtggcggcggacagcgcgacggtcaggggcttgaacgaggtggccccgtcg -ctcatctcggtgatggtgtcgaagaagggctccaggtccgccaccccgcgcgggccgatccccagccatcccgccagccg -ctcgggcttgacgtcgtagcacgagccgtcgatcgcccaggcgccctccttggggtcccaggtccagggcgcgtcgttca -tcgtcgccaacaccccgaaggcgtcgcagcggtccttgccgtcgcgcagcaccccgtagccgaacttggccttgccaagc -atcgtggtccattcgagcaacaccgtcggctcgatgttcagcgccgaaagatgccgggccagacggcgcgtgttggcgga -ggccggcgaggaaatgcccagcacgtcgtgctcgaagatcgcccagtcctcgtagtcggcgaaccggcaatgttcgggat -agtcctcgaacacgcggtcgcggtcgtatttcggatcgtagatgtcgcggaagtcgtagtgccgcccgccgccgcgaatc -agggtggggttcgtgttgagcctcagggcgtagccaagttcgatgtagcgattttggcgctcggccgcgcgtcccagcgt -cgaggaatcaggcatccagcacccggtccactccccttccggtccccagatgaacaactgcgcgatctccgggcggatgt -tacgaaggtgcggctcggtgggcggcagataataggccagatcaccgatcttgaaccgcatgctctggacgtgctgttcg -tagcggcgcacggcgtcgttatagcgaccgcctgaaaaaggctcgatcatcctggtcgccatcgcgtagtccttactcat -cagccagtccatggcttgcttctgataggggtagggctgaaaggccttgaccatcttctggcttatgaccgtctcggact -tcagtatctgagccatggtctcctggaggcgcgacttgccggcttgccggggcgcgacgaggaggtcgcccaggcccagg -gtggtgtcctcgatgatcttgagatcgttccaggacgtcgcgtgcgcggtgacgcttcccacgggcgaagcggggtcgac -cccgaggatcatcttgccgatcttgtggtcgaacgccgccacgatctgctcgatcttcgagagcggcgcggtgtcgtcga -ggggataggccacatcgagcgtgctcgccggcagcggcggcttggcgtaggcttcccgcagcttcatgagcgcgtcggcc -gccttgccggtcggggcgatgacctgggcgatcgccgtttccggcggacgggcggtcttgccgcccaggcccagattgct -caggaaggccggctcaggcggaacggagggggacgacaggctgatcacctcggagatagaggggatggcgcgggtggccg -tccttggacttcccgaggcacttgacctcgacccccgtgatttccgcctgctggaccgcgccataatcctgatccttgaa -ctctccatgcacgccccaggcggcgatcacgtcggcgccggcggtcatggcatattcgaacacgtgctggaggacgcggg -cgttcatcggcccgatcgggtcctcggccgccttcatctccgccggcgagggcgagcggaaggcgaagagattggcgacg -atgatcccgccatagtcgtcccgacgcgcaaagcccatgcagcggcggatcgtcggatcgtccagccgcgccgtcgcggt -cgacgggttcagcatcaggaagatcagcagcggcttgccggggtcccagacccgcatgaggaggtagcggaaggtctcgc -accgcgacagcagggcggccttgatcacgccttcctccatcaccgcgtcgccgtagacgtcggtcaggtcgggatcgaac -acggcctccagcgaggttccgtccaggacctggagcaggcctttccaggtggcttccgccacctcggcgtcgatctgggg -tgctgtcgtcattcctgacatttgccctgaaacgccagggcctgtcaacgcttgaaatcaaaagggccgccccggcggga -cggccctttctcgatcttgtcgaacttcgccgatccgaaaccggggcttcccggcgaccgcctcggagttcgaccttgta -gcgcctttaacgcttgccccgcgtcgcggcttgggagcaccgagccttgacgctgatctagtgggcggcaggtgatcgcg -gcggtcattgcctccttcaagggcgaggccctctcatgcccgcgcagcttaggcggcggcgcggatcacgtcaatccccc -ggatagctggcgcagacctcacgcaggatcgagcgcagcggctcgcccggcaccgccaggggcttgagcttgcggctctc -gtcccaggccatggcgttggcgtgcaggagccagaggacgaaggcgcgcaggtccttggccccgtcgggcagcgggatgc -cgcgcgcggtggggacgtggaagactcgcccatcatccgtgtacgcgagaacctcgtcgagcaccgtggcccgcttcttg -gcctcggcgaggacagcgacacctttctggaactcactgacctggatgagcgcccgacgctccttagggaagtgggtctt -ggtccaccaggagggcttgctgtttgaggacacggttacgctccaggagggcacgcagcgaggggatgtcgccgtccgcc -atctggtagaggcggacgaactcgtcgtagtcgtactcgttgatgaggtcccgcatcgcctgcgggagcttgtcgatggt -cttgaagagccggcgccgatagcgctgggcctccatgcgccggcggatggcggcgtggcgcgtcttggccgcccgaacgc -gccgcatcaggccgccggggcgatccagtcctcgcggtcgtcggcgtagagcaccgccgccagcttccccgtgccgatgt -cgcacttggccgccgcctcgaccgcctggggcgcggtggcccccatgtggagcgcgcccagggccgaccacgtgcccgag -ccgaaggcgtagaacggcgcgcgcatggtgtaggccggcgcgccgctctcgaaccgcaggcaaagaccatcgggcaggat -gatgtagccgttggtctccttgtccggcttctcggggcgccccatgtcgcaataggcgtcgcgcccgccgctggccagcc -actcgtcgaaggccggcgagcgcacccagtcgttgaagatttggacgtaggccgattcacccgccgcgccgaacagcagc -gtgccgccaggacccttgcgcttgccgatcttctggacattcccgcagggcgtccagaggtcgagaacccgagcgtcagc -ggccagcacgccgtcgcgatagacgatacacgtcatacgtccaaactcctcaaaagcaacttcagatcagcgcggggctt -gcggcaggcgcttggccgccgggttccgggccgagcccgtggtcggacccgccagacgcccgaccttctcggccttgaag -ccctcggggcgcaggggcgtgcgcgacttgcccgacgcggcggaccgctccttgacgaggtcatcgccgccctgggtctg -gggcgtggcgcccttgatcacgccgcccttgcggttgacgttcggggagttgaccgactggacctgcccgttggtgccag -ccgcgatctgacgcgtcgtcagatcgaccagggcgtcggcgaaggccgacagcagggccagggcggagtcctcgaccggc -ttggccgagacgccggtgaagccggtgtcctcgtgcttggccttgccgctgatccgcaccgagatcagccgggtcttctt -gttgcggaacaggcccgagacctcctcgcgggtcgagacgtcgacgcgggcgccgggcgcgaccgtttccagaagggcca -gggtcgcgtagtagctgttgacgaaattgagggccgagcccttgggatggccgacggcggcggcgatcttggcgaagccg -ttgtcgatcacggtgctggcgaggctggtcggataggactcggtcagcagattgttgacctgggtcttcagggtcttcag -ttggttgatgtccagggtgagggcgcgcttggcgaccatggtctttctcctagtcctgctcgtcgatctggcgagcgcgt -tgagtgttaccgtggcgataatcgttccagtggtccatcttgacgaacttcccgcccaccgtgcgttggacgaaaatccc -gtccggggagatcagcccgtatttctcgtccgcctcgttgatcatgcggaagaactccgcctgccaggggatcggcatct -cctggagcgacacgcgcggcaggcagagccaggaggcgtaggagagcccgaagaagtagctcgacggggtgtcatgcagc -ggcacgtcgccggcgtagtgcgtcacgtgcccggtctcgggattgcgcgccgaatggctccaggcggcccagagatcgcg -gcggctggcctcggcgtcggcctgaccccggatgatcgcctggacgtctggcgtatagcccgagaaggcggtggtgtcgt -tctcgtccaggcagtcggccagggccgcgcgcaaggccgatcgcagcttgtcctcggtcaaggtcgcgtcggcggcgatc -tgggcgatacggtcgcggaaggtcattggcagacgtccttggcgtcgcgcgcggtcacgggcgacatgtaggtgtcgggg -tcccaggcgccgggcgtgctgccgccatagacatagtcgcccggcgcgggcggcgtcatcgacccgccgttgctggcgac -cttgcccggattggcgtaggccgagagccacaggcgcccgtcgctgccgcgcaggacgaattggccgttctggcggcaga -cgcgagcgatggtcatgcgccatgcgtagttgagcttggccttcttggcggcctcgtcccgcaaccactgctcatgcccc -agacgcgcccagcgcgccttcttggccacgaggtccttgtgctcctgcgaccagagggggtggttgtactcgtcgcacgc -cgagaggctgatcccggcgacgacgagcaggaggagagcgccgcgccgcatcaggcgatctcgtagccggccgcgacccg -ctcgcggatttggtccagggtcgccggctccagcaccttgccggtgttgaagacctcgtccagcaggtcgtgctcgacga -cgtcgccctcgtggaccgtgatggtctcgaagcggccgtcctcggtcgtcaccagggccagcttgcccttcttggagacc -ttgcccggatcggtgatcgggtccttgtagatttcgacccactcgccgttgatctcctgggccgaggacttcatcgccca -cttgttggtgtcgcggtccaggtcgcccgtcgccagaccgccgccggcggccgtgatgatgctgtcgggcgcgacgccga -tgttgcgggccaggatgaacgggtccatgtgggtgttctcgttcatgccgtcgccctggagggccttggcgcccaggttc -agcacgtccaggccgtggctgttcttctgggtcccgaagccggcggccagggtctggacgaccggcgggatgaccttgaa -gaggtcgcccgaatccgggcggcagaccggggtcaggttcttgttggcgatcagttccttgcgctcggtcagcttgccgg -cgaagcggaagatgtcccaggtgtcgccgaccagcgagaagatcgagccgggaggcgccttgttcaggcagtggtcgata -tagtcgtcgtcgttgtcgcgcccgaacgagcacgagatcgagtgctccgaggccaggaccgaatagcccgacatctcgct -gaagtagttgatattcgccgcccgcacgccggggacgttgtccgagccctggaagtggaagaggtgggcgatgccggcca -ggaccgagtggtcatagcccatggtcccgcgcgaggagaagtcgaggaaggcgaacggcgacatcggggtgtcgctgttg -gcttcccagaagctcttgatccgcgtggcgatgccgttgacgcgcgcggcgatcgtcgaggccgtccagacgtcgcgcag -gatcatggtctcgaagtaggaggtcagccagggcaggcgcgggtcgaggttctcgaccgagatcagcgcgttgcggatcg -ggatcatcacgccctcgggcgcggccttgatccgcagcgggagatagccgccgtactcgttcaggatgatctcccagccg -tcgcggttgaacggcaggccgtgggccggcacgaacgcggccatctcctcgacgtcggcgcgggtgaccggcttgccgag -cttctggaagagcaggcgctggaacgccgccagcatcaccttgggatagcgcccgccccggctctcgatgtagctgtaga -cggtggtgcagccgtcgcgatagagcacccagtgccccagcttgtagctgtcggtgtcggcgatcaggttataggtctcg -acgggcggcgtgccgtcccagttggcgaggtcaaaggccatgatgaggtccccctttaagcgttgaggctgagcatgcgg -tccacgatgaaggcgtggtcctcgaaggtgtctccggggtcgatctccgagatcgggtcccagtcggcggcggcggcgtc -gtcatggccctgcacgtgcggcagacccaggcccagaggcgggggcggcaggacgaagtggtaggccgtggagatgatgt -gggcgcgccgcgagcggtgcgggtcgtcgaacacctgcggatcgccaatctgatagcggcgcagcaggtgcatcgccttc -agcacgcagtcgggcgccggcggggcggcggacttggtcttctcggccgccttgcacgcttccagccacgcgcggtactc -cggcagatgggcgggcgggatgaacagcgccgtctcctcgatcacctcgcgcaggcagttgtccatcagcgagcgaccgg -cgttgacgaaaccgcccggcagggccttcattccaaagccctcggggccgccgcgccggatgcgcaggatgtgaccggcg -cactcgacgaccgcgtccaccgccaggaaggggccagcgccccagcgttcgcgataggcgtcctcggccttcttctgcga -catcagataggcgtattccgggcggtcccggaaccgttccaggaagtcgatcgtgctcgggtagaggagatcggtccagg -cgtagccgttgtcgctccacgaggtgtcgcggaagttgacggcgccggcgaaataggccttgcgcagggcggtggcgttg -accccgttgtcctcgaccggggtgtagggccattgcgggaaccacgtcagatattcgctggtggcgtcgcggatgttgcc -gatcagggtgacgcgcggacgcaggaccttggaggcgttcttgacgtgctgctggacctgggcgatccactcgttcttcc -cgtaggggccggtgtcattgagcgcgatcacctcggtgcggctcaggaggtcgagcacgagggcggcgtgatcgtccact -cggctctcgacggtctcggcctcgcggccggcgtcggcctcttcctgggccagatcgctgagcccgttcaggatcatctc -ctggcgctcgcggaaggtgaaggggttgcgggtgtcgcgggcgagattggccgaaccgacgaaccacaggaccttgcggg -ccttgcggcgcgcggcctggaagaggcggaaatgacccatcctggtcaccaactgcccccgcgtgatcagcaccgcgatg -tcgtattcgaagtccactatcgcttacccctcattctgaagccgggccggatgcgccggatcggcttgttctcgtccagg -gagcgacccccatagccgctcaactcgctgaaaccgttcatgcgcaccgcgaaccggcgcgtcttgacggtcaactggtc -gcgctcgaaaccgcgctcgaccagcgtcaggtcgatgacgtcgccgaacacctccccgtggaagatgcgccgccgcgccc -aggcgatcgccgccccgaggtgcggaaattcccggtgccgctcggcgtcccggatcgagacgccgtcggcatagctggcg -tcgacccagtccagtttgacctcgcggcgcggcgcggtcaccttcttgaactcgatcggcggcgacggttggcccaggcc -acccgtctcgatgtcaaaaaccgcgtaggtgattgtctccgtcatgcctcgcgacactacgctttgggttcttgtattgt -caacacatcacttcaggagcttgagggcgggggcgtgatatttgaaccccgcctcgctgatcggccccacgcccacgaag -gtgatggtcggcttgccgaacaccgtgcggcccgcgtcgaggacgagggtcgcgccggcatggtcgcggaaccgctcata -gagggcttccaactcggcgttggtcccggcgtggagcgcgatcttcacggccgactgcgagtagcggtattgccgcgcga -tcctggggaaccgctccatggcgtcccaccacgcatggaggtaggcgtggccggcctgagccgcgagcttgcccaggttg -agggatttctcgtccggcttgcggcggttcttggccacggtcatcgcgtcgagcgcttcctggctcacgacggcgtagag -gcgcagttcggccttaggcttgccggcgaagaccgccatcagagagtcccaggcgttgcgccaagcgtcgatcacgttca -tgaaaagcggctttcgtaggaggcctccagggcgatcgccgcgtcgaaggcgacgtcgatgaggtcctcgtgcatgagaa -catcgaaggagcggtcgacccggagggcgaactgggcttccatcgagcggttgaaggccaggaggtccttgtggagccct -gccatgcggtccaggagcttgatcgcgtagacgtccggcccgaaggtccctcgcgtctgatgcaggcgcttcttgacgtc -gttgatcgtctcccaggacttgaccttcaagtcctccatgaggtcggcctgctgctcgacccggatcaggtgacgcagca -gccgccggagccgggcctggatttgatcaggcggggccgacggcggaggagcgcgacactcctccgcctcggtggcgatc -atctgacgcgcccggttgacgcagtcgaggatcgaagccatcagccctcggcggccggcgcttccggctcagcggtggtc -ttgcccttgcccttgctcgccggcgcggcctgggcttcttccgccgccggctcggcgatgggcgcgggggcttccaccac -cggttcggcgtccgcagccgcctcgaccggcgtgtagtcggcctcgaacgcggccggcttcaggatggcgatctcgtagg -tgtcctcgccgcgcgggatgcggacgatgtagtcgtcctgggtcgccgaggcgatctggccgttgatcgggaccaggagc -ttgccgacggcgtccttgccgacgtgcatggtccccatggcggtgtagcccgagtgctgggtcagccacgccggcaggtc -ttccaggcgctggaagctgtactggacagcgtccacggtcaccggttggcggatatactgggtcatgcggtctcctgctg -gaggttagccggcgccgggatggcgtcggaaagggcttgctcgaccaggaccaggatgtccatgacgagcttgggattga -ggtcgggctcggtgagcgcggcggccagggcgttgatccggaaccacgtcgggtcagcgtgcgggatcagattgagattg -tgcaggtgcagcagcgtcgagccgtgggaggcggtccgctccgaaagctcgcgcagcacgcgggcgccggcgagttggtc -ggccaggaccttgatcacgctgcccgagggagccaggagcaggcgcatccagtcgccgttcggatcgtcggcttggcgca -ggtccggatggtccagcgtcttgccccagatcacctcgtgcgccttggcggccagcgagcggcggcggcgggcgaggtct -tcggcgtccttggcggcgcgcaggctggaaagcgtcgtggcgatcaacaccgagggaaagagcgcgacgacgaagaacgc -ggcgcgctcaagtggcgaggcgtgcgaagccacgatattcatggccgtgccgatcagcaccgtcggatagatcaagccgc -cgtggcgctggatgaacgagatcatgaaaagggcctccggcgttgtcgtcgaaggcccttctagcgagtcggtgtcaggc -tgtcaacacatgtcagccaagatcaggcggcgttcgtcaccagggtttccaggcgatcaaagcccagatcgaggcgaccc -cacatcgacgagggcgtatgcggcttgaccacctcggtgaaccgcgcgcgctccttcagatacatgcgggccatggggat -gttcggctggccggtcgccgggtccttgatcgaggcctcgacattggcgatccggtcggcgagcttgaggatgcaggcct -tggggtgctcgcccagcttgcgatagatgtcctcgttgcgggccttgcggttggggccaatgcccgagaccgcccagacc -agcgctgcgacgtcctcgccgaacttttccttgatcatctccagccgctgctcgggcgtcatgtcgagatgggtgtcctc -gatcacgtcgtgcagcttggcggcggccgtccaggtaaagcccaggaagccgtagtcgtcgaggatgcgctcgaccttct -ggagatggtagagatagggctggccggcgtactgctggtccccgtgggcggcgatggcgaattccgtcgggtcttcctgg -cgcagcggcgcgcccggcgccgtcggaaggcccgtcaggatggaggcgagttggtcgagcgaggcgtcagacatggggct -tctcggagatcggggtgaagacttccaggccgtcgacgatctgcatcagatgcgtcggcgggtgggcgggattgtagcgg -atgtagccggcgaggccgccgtcgatcatcgccccgccccgctccttgtagtcgtgccggaagcgcgagaccaggaatga -gccgtcgggcatctcgatcgccgagaactgggcctgtcggatcgaggccgccgaggtgatgtagagcccgccgcccagcg -gatgggtgaagagcccgaagtagttgtcgtggcccttctcgcgatccggcgtctcggtgtagaagacgtggaacggcccc -tcgcggtcgggcaggtcgtaatagccgacgtacttggcgttgtagtgcttttcggccccggcgatgttgatgctgctcat -gcgaccctcaggaattctccccaggcggggagggcgtgcttcagataggcggcgtgcgcctcgtccggcgtcgtgtagca -cccgagatagcggtacaccccgttgatcgtgacctgggcctggaacggcttcgtcttgctccggctcttggtcacgccct -tgggaagcgcgccgacgttcgggcggttcacgaggttctgggaccgcgtcgccttccggaggttcttgatccgattgttg -cgtcggttcaagtccttgtggtcgacatcgtgatcgggcatcaccccgtggtggatcgcccaggccaccttgtgggcggc -gatttgaattcgccggccgccataggagaccttcatcacccgatagccgtccttggtcaccgagccgcagcgcttgcggg -acttggagccccgcacggtgatggcgccggtggcgggatcgtacttgtagcgcgcccggaggaagtcgaccgggatcgaa -aactctgcatcccccgacataggattagtccttctgggcgtgccgcttgaagaggaggtagaagccgtaggcgacgagca -ccggaatccagagcaggatcagggccacggtctgaccgagggtcatgaagaagaacgcggccttccagtcgttgttgtac 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-tcggcatcgaggtctccttcgttgtcgtcatgcggcttctaggtcgactttgccggattgtcaacacattccagccagcc -gggcgatgtagtcccgcatcgccgcgctggacgcatagcgccatgtccaagggacctgctcgggccgcgcgccgttgaac -cggcagagccagaggaaggccgcctcggaatggggccagttctcggcgtcggccgagaaaccggtcatgcggaagcacgc -cgcgacctcggccggcgtcaggttcgggtcgcgcacggccttgagcttgaccttcacctcctcgggcggcgcgggtggcg -ggggctcgacctcgtagccggcctttcgcaggagcttgatcgcggcggcgatctcaggactcggtttcaggtttccactc -cccgcaccaggaattcatgtggaccagcgggaattccgcccagccgatctggtcgggcgggttgtccccgtggaagctgc -cgcccgttcgcgcggggtggtagcgcgacgggccgaccttgatcgagggtgggaagcgccggcagtcgccgtgcatctgg -accgcgcccgtctcaaggaagaaccggcaggtcttgcaggattgaccttcgggctgtctcatgcggggaccctgccggcg -ctgacggccgcgcgccaagcggcgacgtcgcccagaaccgcgccgcccaggaagcggtcctcatggaccggcacgtcgcc -gtcggccagcgccagcagatcgagttgggcgtcgatccactgctgctcgctcatatagggctggtggcgcgccgtggcgc -ggatgccgtattgcaggcgcttgtcgtagagggtgagacgcaggcccgcgtggtcgcgctcgatccagatgtcaggccgc -tgcatcggcgacctcctcgacctcttcctcgctcggggcgatcgtcgagcccgaatattcctggaggtggtcgaccgcct 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-cgtcgagggggttctagccggcgaccgcgaccttgtcaacactctcgcgccagttcttaatcgcttggcgttccgcgaag -gtgggctggcgctcccagcaggcatactgctccgagcctcgggtacagttctcacggatgatctcgccatccgcgttgtg -tagcggcgtgtagggcttcttcatgcagtgcccgagatactgccccacccaggggtgccagaggcggcagttgccgcaga -cctgcctcatcaggcgctcattatcgccgcgcagaggatcatcaccaccagcccgcctacgatcgggcagacgatcagcg -acatgcagaacgtcaaggtcgggtggtcgatgaaatagaacaggtagggaggcggttggggctggttatagagaacggcc -gcgcccagcgccagcgcgatggcgccgatgatccaggccagtccataccagaaggcgccctggagaagcgtttcgacttt -cgggttcatcagcggttgttctccaggtcccagatgcggttgcgcagttggcggatggtctcttccaggtcgcggacctt -gcgataatgctggtcctcggtctcctgggtgttgcgcttgtagcgccgctcccgctcgtccatctccgtctggagcggat -tggggatcacgtcatgaccgtgggccatgccgtagttctcgaacgagccctcgatcccctcggcgatcccctggcgcttt -tccagtgggatgccgttccagaggtcaaagaggccttcggcgtcaaacgaggcgtccaggctttcgagccagtaatcagt -cgccacgatgcacgccctccccggcccggacgcattggatcgggcctccgtcgccctcttcggtgtagcgcacgagactg -ccggccttgatcagcatctggaccgtctcgtcgctgaccgtaacgtcgcgccccggcgggctccaggagcggccgtcatc -catcaggatcagaccttcgcgccggatcgccagggacatcgcctgggccgcgcgctgggcggcgctggtcgcgccctcga -ccaggaccttgaggtcctcgatcgggaagcactccaggaaccgagtgcggacctccaggcgctcggccggcggcaggcgc -atgatgtcgcccaccaggatgtcggcgtactcctcggcggtcttgggggcgtcggtcatgacttgaggctctggcaggcg -aacgtgatcacgtcgccgagggtgttgaaatcctcggggaactggaccggctcagggacggcgaagtcctcctccaggca -catcatcaactcgatgatgtccaggctgtcgaggcccagatcatcttccagccgtagcccctcgtccatatcgtcgaggg -tgtacgaccggtcggtgatcgcatgggcgtagtcgaaggtcgccgccttgatctcgtcgcgcgtgaaggtcacggctctc -cccctggtgtcgtttcggcgcttctagccctcccaagcagagccgtcaacacatcagcgccacgccagacccaggatagg -ctcagaacgaggtcgcggtcctcataggcggcgctgcgcccggtgatcaccttgatcgccgagagcgggccaaaccgcca -gaagacgaccgtgcgcgagtcgttgcggccgggcaggtgctccagcagcacgcgacgcttgatcgcgaggtggcgctgtt -ccttgtggaggaccagggcgatcttgcatgtcggatcggacccgaaccaccggcgccagtagcccggattgtcgatgttc -tcgtagagccggccgatccgtttgctgaccgggcgcaggcccggctcgcgccggcgcacgctgagcggcgggaacgtgca -gggcggccactcggcgagcaagctctggcgcagccggcgaaattcccaggccggcatggcgttgtccttggtgttgttgc -acgccacgcaggccgccgccagattgctctcgtggttcgatccgccctcggccttggcctccaggtgctcgatcgtcact -tcgtcgggctccagcttgccgccaccccggccgatccgccggcgataggccatctgccccgtgcaataggtgcagaggcc -gcccgcctccaggaagaggcggtggcggcggttcggcgcggcgggcggtagcgggtcctggaccagcacctcagatgagg -acatagccgtccttgccgttgtcgaagatcagatcggagaagcgcagcgtctccagggcggtgttgaaggccgcctcgga -gccacccacccgcgcccagaccgtgcgtccgcccatgacgacatggaagaggtccggcgccgtctgggagcgcaccaccg -aggcggcgttgtcgaccagcacccgataggccgcgccggcgaccgtcaggcggtcgcgcgtgtcgagcaggcccagaccc -cgcaggtcggcgagatagtcgctcagcccctgcaccgtgacgccggccgccagggcaagcgtggtcgggttgttgttggc -gcccaaggccttaaggacctcgacccggcgcaggatcgcctcctcgcgggtctcgacctcgatctggtcgtcggtcttct -gggcgccctgaatggtcttgcgcagcggttgcagcatggtcgatccttaacgaatgaggctccaggccttttgggttttg -ccgtagggttcggggaagatatagcctcggtggtggaggtcggccaagatcgcctcggtgtgcggaaggtaggcctcttc -gctcccggtatagggcgtctcctggttcctggctcgccagaagaggcggtggttcagccgcagagccgtgcgctcgaacg -ctcggcgcggattgatctcgcaggccaggatgtggcaaatccagcccgcctcggtgtggcgcacccgcccgccctgcaag -gcgaagaagccctcgtccttaagcgccatgaactccgcctggagttccggcaggaagcgcacgaggcgcccgaacgcgtc -atggaagacgacgacgcggcgatcatacatcggcttgatagcccaggaacgggcgcagaaagcccatcaggtccttgtcg -atgcggatcgccttgagttccgagcagcgggcgttctcggcgacggtgcgtagccacttcgcccgctcgtaataggtcgg -ggcatgatcccaccagcgatagctgctctggcggatagcctcggcttccttctcggtcggcgggcgtcgcttgaaacgcc -accacggcccgtcctggacagtgtccatcgtcatgatcttggccagggtctcgttgcgggtcgcattgcccaaggcctgc -gcttcctcggccgccttgagagcggcttcgagcaggacgaggcgatcgacttcggcggacatgctcacttcagcttctcc -ccaatatagacgtccaggaaccgcgcttgcgcatcctggtcctggaacatccagatcgcgtacttggtgcgcgggaacgg -ctggcggaagaactccaccgggccaaggaggtccttggcgccgtgcggcgtcggcgcgaccagcggcgtcttgaccacga -acgggaagcgttcgaggcgcttgatcaccgccatcgaacagtcgcgctcgcgcgtcgtcttttcgggcaggtcgcgggtc -caggtcgtggtcatcaggcttgcacctcgaaggcgttgatcttgtgggcgtcataccaccagcgccggccctggcaggcc -ttgcaggtgacgtcgtcccagccctcggcgaaggcgaggggcttgagggtatgggccggcaccgtcttgatcgtcgagcg -caccccgccgttcttcaggtaggcggtgcggccatggaccgtctcgggcacggcgatcgtcttgtccggcgaccagcgat -tgcagaccgtgtagcgcccttcgccgctgttgcggaacgggcgcggggcatgggcggtggcgggcttagacacgggcctt -ctccgaggtccggatgatcagggcgaccagcaggatcgcgatgatcaccgccgtcgtcatcggaggctggcgattgtagc -cgtcgatgaagccaagcacggtccccgccagcatcgccgccccataggcgctccagaacttcaagcctcgatctcctcga -accgcccatccatgaattcggcctcgcgccgaccccacatctggccctcggcgtcgaggtaggtcagcagggtctcgtca -tcgagcaccggggtctcgcactggatgcggatcgtcccgaccagggcgtattcgccgccgcgcttcctgtggcggaagcg -ccgcatgccgcgcggaagctccgccaggaaggccttcagggcgtccgccaccttggcgacgccgtgcgggaagtgcgagc -ccggcccgcgcacccattgatagatcgtcgccagggcgaagcgcccggcggcgatctcgcccgtggggtccttgcggatc -atgtccggcgcgtagtcttcgagatagttcgtcccgaggatcgccatgcagcgggcctcctccaccgaggtcggcagacg -caggtgatcgcgatccaggcggtcggcctcggcgagcgacttgatcaccccgaccaggatcgccgccttctcggcgtgcc -actgccgtccgcccggctctggggcgcgctcggcgtggtagaggtggtagtccagtatctcgtggacgtcttcgctctgt -cgggacatagggttccttccgttgtcgtcacccgcgacactagatggtcggaggtgtgactgtcaacacttcacgtcaga -gctagacggcgacgatagaacaggcgccggccgttgaagaacagacggatgcggaattcctcgtcgagggtcccgatgtc -gaggctaaagcccaggaggcccaggctgacataggcatggcgcccgaagctccccggaatggcgtccatgccgccggcga -cgaaccggatgagccagagccagcccaggtcgaatcgcttgaagccctgccattcgatcgagcgccaggagaagccgccg -cccagcagggtgatgtcgatgtccaggttccagccgtcggccagcggatcgcggcggcggtggtagcgcaggcgaaagaa -gccgccgtcgaggtcgaagttcgggatcgcgccaaaagccagacggcgcagacgcgccaggacatagccgaccgggaaga -tcaccagggcgtagagactcaggaggaagaccagggccacggcgcaccacaggccatgccagaagaacccgagcatcatc -ccaagctttggcgaatggtcgggcatggtcaggtccccttggcgaagtcaccggcccggccgatgacatggaaataggcg -taggcctcgccgggcgtatgccggtcgcgattatcgacgaccgggaggtcctcggcgtagcgggcgaaccacgcggcctt -gcgcgccgcccaggcggcggggtcctcgtcgtgatcccagccgaacagtccgcgcccgttttcccgacccttgcgcaggt -gggccactggctggttggtcccgatgtagcgggtgtaggcctcgggcgcttcgccgtgctgggtcgggcggccgtcgtca -tggtggtcgacgaaggccagatcgtttttggagaggtcctgggcgatccagccgcgacggtccttgacgaagggatcgac -caggatggtgatctcgcgatagatgttcgcgccgacgatcatggcccaggcctcgttatcggcgcgttccttgccgccat -cgcgcagggagatcaggtaagcgcagccgtcctggatggacttgccctccaggagggccgcccagttcatgcagatgtcg -ccccacttcttggcggccaggacatcccaggcggtgcgctgcttggcgtcgcgctcgtaatagaccctggcggcgtcgcg -caggtgatcggagaaggtctgggtcatgttagtagccgtcccccttggcgcgattgagttggtcaaggacgcgttccgcc -tcctcttctttccgccagcggccttcgatggttttcatcttggcggcggcctccaggtgacgggcggcctccttcagctt -cgccgccttggcgagaagcgtctgggtcgccgtcttgtcgccgaccatgacgaattcgtcgatgatctcgccggtgcgaa -tgtcgatgatgcggaactttttgggataatcccgttcgcacggatcggtgttggcgagatagtcgccgcgcgccctggcg -tccttcagcgtgcagccgccggagtgatcataccagacggccgacttggtgtagttccgcccgtaaccctggaggacata -gaccggcagttcggtctcgccatcctcggtcgcgacctgcccggccatcgtctcgggatagaccacgaggccggtgcgaa -tgtcgatcacgcgccaggacccttcgtcgccgggggtgaagacggcgcagttaggcttggcctcttccagcgtcgcgaac -gacgaatggcgcttccaggaccgagacgaagcggggatgtgtgggcgatcgccgtagtagcggttgttcggcaggggata -gaacccctggagccagtacggatcgtgagccagcgcgcccatcagtcgaccttcggttcgcgcttgaagcggccgttctc -gtcatagcggtccgggttggcgccgggggcgtggaagcccgccatcgagccgatctccatggccgcgcgctgcgccggcg -tgacgcccatgcgctggttcatggcggtgacggcggcctcgccctggaccccgtagtcggtcgcgtagtagccggtctca -tccttcttcaggatgaccgtctcgcccgtctcgatgttgatcgagtagcagaggtcgggcagggccgcgagattgatctg -gcgttgggtcagcatggaggcctccttgttgtcgtcgaggatggcttctagccggcccaggtcacgttgtcaacactcga -cagccaagtagacgttgcgacgcggctcataggggagatcgttggcgatcgccatcagccagccagcgtggcagcgcttt -ggagcgcagtggcagacgaggtggaagcccttgaagttggccttgacccaggcgacgaacgcctcgtccttggacttcag -ggcgatgtacttgtcgatcaccgtgtcgcgatcgccatcctgaccgatgcggaactcgttgcccgccggggtccctcggc -cgacgtacttggacatcggcgggagatggcctgggaactcgcttcggctgagaacgcgcagttcgatcatgccgcccggc -tctccacgtagtcggcgaggatcgccagggtgtcctcggccgaggtgtggaggatcgagaagcccccagcccggttccag -gccacgcagttggcgacgcggtcgtcgatcaggatttggtggtcggagtgcttgcggtgcatgaattcctgcttcttggc -cgaggtcgtgcagatgaagcggtggtcctcgatccggatgcgatcgggcaccatgccggccacggcctcgtccccggaga -acatcttggcgaacgcctcgggcagaagcgtctcctcgatccagcgccgcttgccataggccgcgcccagccagtagggg -tggatcaggaagtcctcgtccgtcgccccgaacttgggcgaggcggtcaggatgatcggatcggcctcgaacaccgccgt -gtagaggtcgacggcgccgggcatgaacggcagggtctcgaagaagttcgtgccctcgatcttgcggtacatcccctgct -tccagaggttggcttcgtcgtccatcgcgtggctcgacttgttgtactcgggatcgggctcgaacccgagccggcggatg -ccctcgtcgaaatcggccaggacgccgtccatgtcgagatagatggcgaagttcttcaggttcatggtcactccggaaat -tgcgcgtgcagccccatggcgatgcgcgccagttcgtaggcggtcttggtctccaactcgcgggtcggcgtgcgctcgat -cttgagttggtcgctcatcatgtggatggcgtggatgatgtcgctcttgcgcctcttctcgtagtagcggtgcgacgcgg -tggcgcggatttcgacgatcgccatcacagggctcccgcgcaggccagagccatcgcccagccgcgctcggtcggctcga -agcgggcgattggccccttgacgttcggatcgtcggagaaatgcgggtcgagccagcccttgttggcgtggatcacctcg -tcgagcgagcgcgcctcatagaccaggattttgcggccctcgtagttgagggcgtcggggtacatgatctcgaccaccgt -gcagcggccgacctcctggccccggatgagcctccagcgcgccgggtcgggatcgcccggcgtcagcgtcacgggagact -gcccgccggagaaaagccgcatcttgctgggctcacgcgccgagcgtccggtcgagaacaatcgcatccccaccctagtc -tcccaggccctgcatggcgttgtcgcgactgtcctcggcgtcgggccgagacgccagggccgccagaaggtcaaccgaga -ggtggcggttgtagatcgccacgcccttatacttgaaaagctcgctggcttcgtggatcagagcccgctcaaccgccgcc -caggccgtctggacgatctcggtgtcggtggcgtagtaggagagcttccacttgcgccccttccacatctccggctcgcc -ggtgacggtgttgaccccgtccttgcagacgatctggagccagacctcggtgcggctggtcccgagtcggaactcgaagc -caggatagctcaggcggtcgacgatggtgcggatcgattgggcgctgcgacgattcgccatgctcagggcctcgacttga -tcagcttcttcttgcgtcggggcgggcgcggcgcgagcgggaagccgtgatccgcgtacacgggttcgggcggcggggcg -gggaggtccgccgggcgttctaggctaaaggcgtccgcgtcgaggtcgtagatcgacacccgatcgctgtagccgtagcg -gttgtcatggtaggtgatcccgacgtctcccaggctggagaccatgatcacccggcaggccttgcccttgtagcggccgt -agagcttcggcatgaagccggcctcctcgatcgccagggtctcggtggcgttgccggcgttcagcgccaggaagccccgc -acgatggccggcagcttgtagtcgcagatcgcgcggctgttgctgacctcgtagggcatgccgatcttgccctccatcag -ggcgcccaggacctcggcgtcgctcagggtttcagtctcggccataggtgatcctgtacgggagcccgccgacgcagatt -ttcccgcgtcggccgtcggcggtggtgaagcggaagccctggcggttcttggtgccggcgcaggaccaccatgcgcggtg -gaagctgacgacctcggcgccggtggcgcgctcgaccagatgtcgagcgtgacgcccctcccaggtgtaggcccagaccc -cgatggcgaagaagaccagagtcagggagccatagacggcccctttgacatagtcctccatcaggccgccacgagcccgg -tgatcacgtcggtgacgatgcggcgtttctcggccggcatgcccgccagcgccaggatcgtcttggcgccgatctcggcg -acggcggtctcgacgtcggcccggccgtcggtcaggaacgccggatcgtcgaccggcggatagaagtgcccgatgtcctt -cttcaggaactgggccgcctcgtagagcttcgaggacgagatgcggttgtgcccgcgctcgtatttctggacctgctgga -aggtcacgccgatcgcctcggcgagttggccttgcgagaagccggccgtcttgcgggtgtcgcgcaacttgcgccccaca -tagacgtcgacggggtgcggggtcttgtcgtcagccatgagcggcttcctccttctgcttcttggaccgcaggtcgcggc -ggtgcttaaaggccgcgcgcagggcctgggtggtgtcgtcgtgcatgcccaggtccgccccatcgggcgcgaccacgctg -ttctggagaccgaaccgatagccctcggccgtcagttcatagaccgcctgctcctcgtgcatctgggcgaggtggcgata -atattcggccagcgccagttcgtagtcgcccaggaaaaggcgcgcgttgcgctcgacgccggcgacctcggcgcggaagg -tcagcaggaaccgcccaggcccgacatgcgtcagcttgtagccgtgttcggccagcacctcgtcgacggtcttggtgacc -gtgtagatatggaaggtgtagacggcttcgatgtgggtgtcgtcgtagagatactcggaccggttttgatgctcgccgat -gtagggaccccacttgtggtagcgccagccgccggacgcgggctggtgctcacgccggacttccaccatcgagatgaagt -agggcgtgtccggatcgtcgatcaggtcggggatgcaggcgagaagctgctcggggctgtcgcagacgccgtagctttcg -accagataggggatgcgcctatagccctcggggaccggcgggacctcgtccaggtactcggtgtcgagcacctcgatctt 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.xmfa Fri Sep 07 11:30:11 2018 -0400 @@ -0,0 +1,6309 @@ +#FormatVersion Mauve1 +#Sequence1File dataset_9.dat +#Sequence1Entry 1 +#Sequence1Format FastA +#Sequence2File dataset_9.dat +#Sequence2Entry 2 +#Sequence2Format FastA +#BackboneFile /tmp/tmprlpq7n/files/000/dataset_10.dat.bbcols +> 1:83043-149557 - dataset_9.dat +acagtagtacctaacccgactccgaatatagttgtgtaatccttattcttgttcagtctaaaactaatcgcagtaggtaa +gttggccttaatccgcccgcttacaatatctgcactaggatactgggtagccaccactaaatgtatacctgttttc-ctt +gccttctgccctaaccgagcaatataatcttctacccctttgtcaacagcacgtaaatctgcatattcatctacaataca +cactagatagggtaacggctcctccgctacttcattatacaaagataacaacttcgtacctttttccttcataagagcat +atcgcttatccatctccattgtcagccctgctaatacttggcaagcttctttagcatctgtcactacgtctagtacgtgt +ggactatcctcatacttacttagctctaccatagccgggtcaatcataataaactgtagcttttcaggtggatacattaa +catcatgcttacaataatcacatttacgaagaccgacttaccgctacctgttgtccctgccaccaataaatgtacacatt 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+ttgacgccctggccaaggccctaagcgagccgcgccaagccgtcgcccgcgtgaccaaatgggagggcgcgggccatagc +ttcgccaacctgcaacgcgattatgagcggtacggccccggcgcccgctcatggttcggccgggctgaaatgcgcttctt +tgggacgcgcctagaggccgcgccgctggatttcccggcgctgggctgcaccctctttctgacctccgaaaccccgcccg +gcgccggccgggtctggacccttcgcgcctatgtctgggcttcggccgatatcaccacgctaacccatggcgacgaaacc +gacgcggcgaccgcgcaagcggcctttgacctgctttggcgggtcctttccggacagtaaccttttgttaacttctgccc +gctagggtcttcttgcggccgggcaatcccgcccggccgcatcttggagacagcgcccatgacccgcgctcaagccctcg +ccgacatgaacgcccttcccggtatcatcgcctcctttgagcgcgagacgggcgaatatcgcgtgaccctgcgctttggc +ccgctccccatggggcgcggcgcccaagagtggatgcgcgcgcgccgcgaagccgtcgccagctacagcgacgacaaggc +cgacgccctggccaccgcccgcgacatgtccgcccgctgggaggcgatgagcgccgaagagcgttcgcgcctctatcaca +accccgcctaagaccccgcgcgccgccctggccttcgccggggcggctccctcaacccctcgcaaggatcgcaccccatg +accgcccgtaagcccctgaccaaggaacaaaaggcccgccgccgcgcgacccgccgcgccgcccgcctcaactggtcgga +tgagcgccgcgctcgcgaattcgagcgtcaagcccgcttcttcctgatgatcgccacccgcgcccaaggcgccggccaag +gccaggaagccgcccgcctcgccacggtcgcacaacgcaaggtgactaactggcgcatggcgcaggcctgcgcccggatt +aacgccctggccgcgcatccgttcgcggccgtggtcgcctaaggaggcccgcccgatgacgcaccctcacgccctggcgc +tgatcgccctcgccgaaaaggtgttaccgcttacccggctgcacccgctcgaccaacgcgccgccgccgtcgatctaatc +ggcgacctctaccgcctcgccgacgatatcgacgcgaccccgcaagcccccgccctgacgcaaccgaaggccgcctaagc +catgaacccgaaccgctaccgcctcgcgccccgcgaccgcttcagccgtgagcttgccgaaacgctctatcaggcggccg +aagccgtcgcccgcgtgattccgctcatgccggagtccgcccccgatgagcgccgcgcgctgggcaaggtccgcgccgac +cttctaacccatagcgccggcgcccttgttcccaagccgccggccgccgtgctcgaaaccctcgtttgggttgtcgagat +ggcgcaagatcgcgcgactaacgccgatttcaacaccgcccaagaaggactcgacgagcacgagtccctagcctttgtcg +ccgactggctggaagccgaaggccaggacgtgacgccgattcgcaacgcgcaaccgtccgccgacgccctggccgaactc +gccgcccgccgcgacgccgaacaagcggcgctagacgccttggaggccgaagccctggccgaagcgccgggcgacgtgat +caccgacgccttgcgcccctatctgggcgccgccctggccgaaaaccacgccgacgacgtgctagacgccctcacgcgcg +ccggcttccaaatcacccgcaaggaggcctaaagcccatgaccgactccgccaagatcaccggcgcgctcgcgctactcg 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+gaaaaattcctcgaagctcacaaagttgttttctggctgcttttgctggcctgtttgtggcgcttttaacggtttgttaa +cccctggccctctagggtcgaattcccggcgcggcaatcccgccgcccggccttccttcggagcttctgatcatgttcgc +ttccgtgacccttcccgcccatgacgcccaaggcctgagcctcgaaaccgtccacatggttttcgcccgcgaactggcgc +aacatttcgaccacgtgatttccgcccccgtggtcgaaagctggcgcgacgaggacaccggcgccgaccacgcgcaagcc +gccgtttgcttcaccgtctcggcgacccccgccgcgtgggaagccaagggcgggcgcctcgcgcgccggctggaaaacct +cgccgcgcgctatgccgccgactgcgacgccccggccctgactgtcacccactgcgacggccaaacggtctatgtcggcg +ctctggaagccctggcgcgccccgccccggtgcaaggcccgacccgtgaggcggacccggctttcctcccccgccagcgt +gaggacaaggccgcccgcttcgatcgcctgaccgcctagcccctggcctccccctagcgcaccgcccctagaaaggcggt +gcgcttttctgtgtctgtttacttgttgttaaggaatagcctgctagtgtccccttgttggcggacgcatcccgcgcccg +cccctttctggatcgctccccatggctcgcccctctgacctgctcaacgtcaacgccgcccgcgtcctggcttgccttga +gcctatcgccgccgccgctaagaccgccccggccgccgaccgcgccgccctttcctacctgctcgacgctggcgagtatg +tcgccgcgtggcgccgcaacctcacggaaaccgaccgccgcaaggcctatggcgcggcctgcgccgccgaagccctggcg +ctcgctaacgcctatcagcccgccaccctgcaaggcggcgccgtccgccgcgctctgggcgcctatgccgccgccctaaa +ggtcctgctagacggggagccggtcaaggcggtgcgcgccgccgaaggcgcggcgctttcggtccgcgctcgctacgcca +acacccgcctttaacctcttgttaacacctcccggctatggtcgggaggtcgcaaggagacacccgacatgacccgcccc +ggccccgcctcgctcctgaccccgcaagcccgcttctcgtcgccgcgcgtcctgatccttccgggcgcggctcccatgcc +gattcgccagccgcgcggcctttgcgccgtcgagtgcgtcgcccttggcgtgacgctgggcgcggcgctctacctcgccg +cccgcgtgttcggtctggtctgaccagacccccgccccgcccccggtcggaccggtcgggggtgtgtcccataatgacac +acccccgccacctagtatcttttttgattcggagggacccaaaggccccctacgttaaccatttttggcggcgccccc +=
--- a/tool_dependencies.xml Wed Aug 17 14:46:55 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="progressivemauve" version="2.4.0"> - <repository changeset_revision="0aeb3a1b5106" name="package_progressivemauve_2_4_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="python" version="2.7"> - <repository changeset_revision="8b09fe018cac" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="biopython" version="1.65"> - <repository changeset_revision="030f1a505d40" name="package_biopython_1_65" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bcbiogff" version="0.6.2"> - <repository changeset_revision="8ee2210f6074" name="package_python_2_7_bcbiogff_0_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>
--- a/xmfa2gff3.py Wed Aug 17 14:46:55 2016 -0400 +++ b/xmfa2gff3.py Fri Sep 07 11:30:11 2018 -0400 @@ -1,12 +1,17 @@ #!/usr/bin/env python +import argparse +import logging import sys + +from BCBio import GFF from Bio import SeqIO from Bio.Seq import Seq +from Bio.SeqFeature import ( + FeatureLocation, + SeqFeature +) from Bio.SeqRecord import SeqRecord -from Bio.SeqFeature import SeqFeature, FeatureLocation -import argparse -from BCBio import GFF -import logging + logging.basicConfig(level=logging.INFO) log = logging.getLogger(__name__) @@ -131,6 +136,10 @@ # Ignore 0% identity sequences if pid == 0: continue + + # Support for Biopython 1.68 and above, which removed sub_features + if not hasattr(other['feature'], "sub_features"): + other['feature'].sub_features = [] other['feature'].sub_features.append( SeqFeature( FeatureLocation(real_start, real_end),
--- a/xmfa2gff3.xml Wed Aug 17 14:46:55 2016 -0400 +++ b/xmfa2gff3.xml Fri Sep 07 11:30:11 2018 -0400 @@ -4,19 +4,23 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"/> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package" version="1.72">biopython</requirement> + <requirement type="package" version="0.6.4">bcbiogff</requirement> + </requirements> <expand macro="stdio"/> <version_command>python xmfa2gff3.py --version</version_command> - <command interpreter="python"><![CDATA[ -xmfa2gff3.py + <command><![CDATA[ +python '${__tool_directory__}/xmfa2gff3.py' $xmfa --window_size $window_size --relative_to $relative_to --sequences #for file in $sequences: - "${file}" + '${file}' #end for -> $output +> '$output' ]]></command> <inputs> @@ -39,7 +43,7 @@ </outputs> <tests> <test> - <param name="xmfa" value="1.xmfa"/> + <param name="xmfa" value="2.xmfa"/> <param name="sequences" value="karma.fa,phagey.fa" /> <param name="window_size" value="10" /> <param name="relative_to" value="1" />