| Next changeset 1:54a6fb045aea (2024-09-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain commit b20df9521808e2519d001b390545667368111964 |
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added:
axtchain.xml test-data/hg38.chrM.fasta test-data/hg38.chrM.mm39.chrM.axt test-data/hg38.chrM.mm39.chrM.chain test-data/mm39.chrM.fasta |
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| diff -r 000000000000 -r ac3bae00a350 axtchain.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/axtchain.xml Mon Aug 26 17:34:26 2024 +0000 |
| [ |
| @@ -0,0 +1,92 @@ +<tool id="ucsc_axtchain" name="axtChain" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT"> + <description> + Chain together axt alignments + </description> + <macros> + <token name="@TOOL_VERSION@">455</token> + </macros> + <xrefs> + <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref> + </xrefs> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">ucsc-axtchain</requirement> + </requirements> + <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command> + <command detect_errors="exit_code"><![CDATA[ + axtChain + -faQ + -faT + #if $minScore + -minScore='$minScore' + #end if + #if $scoreScheme + -scoreScheme='$scoreScheme' + #end if + #if str($linear_gap_options.linear_gap) == "linear_gap_file" + -linearGap='${linear_gap_options.lineargap_input}' + #else + -linearGap=$linear_gap_options.linear_gap + #end if + '$in_axt' + '$in_target' + '$in_query' + '$out' + ]]></command> + <inputs> + <param name="in_axt" format="axt" type="data" label="Alignments" /> + <param name="in_target" format="fasta" type="data" label="Target sequence" help="Make sure you are using the same name in both alignment and source sequence e.g. hg38.chr1"/> + <param name="in_query" format="fasta" type="data" label="Query sequence" help="Make sure you are using the same name in both alignment and source sequence e.g. mm39.chr1"/> + + <conditional name="linear_gap_options"> + <param label="Specify type of linear gap costs to use" name="linear_gap" type="select"> + <option selected="true" value="loose">loose (chicken/human linear gap costs)</option> + <option value="medium">medium (mouse/human linear gap costs)</option> + <option value="linear_gap_file">Provide a dataset with linear gap costs</option> + </param> + <when value="medium" /> + <when value="loose" /> + <when value="linear_gap_file"> + <param name="lineargap_input" type="data" format="tabular" label="Read the linear gap costs from" help="See help for a sample file"/> + </when> + </conditional> + + <param argument="-minScore" type="integer" optional="true" label="Minimum score for chain" help="Default 1000" /> + <param argument="-scoreScheme" type="data" format="tabular" optional="true" label="Read the scoring matrix from a blastz-format file" /> + </inputs> + <outputs> + <data name="out" format="chain" /> + </outputs> + <tests> + <test> + <param name="in_axt" value="hg38.chrM.mm39.chrM.axt" /> + <param name="in_target" value="hg38.chrM.fasta" /> + <param name="in_query" value="mm39.chrM.fasta" /> + <conditional name="linear_gap_options"> + <param name="linear_gap" value="medium" /> + </conditional> + <output name="out" file="hg38.chrM.mm39.chrM.chain" /> + </test> + </tests> + <help><![CDATA[ +**What it does** + +`axtChain`_ is a tool to chain together alignments. The `chain`_ format describes a pairwise alignment that allow gaps in both sequences simultaneously. + + +sample linearGap file (loose):: + + tablesize 11 + smallSize 111 + position 1 2 3 11 111 2111 12111 32111 72111 152111 252111 + qGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 + tGap 325 360 400 450 600 1100 3600 7600 15600 31600 56600 + bothGap 625 660 700 750 900 1400 4000 8000 16000 32000 57000 + + +.. _axtChain: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt +.. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html + ]]> </help> + <citations> + <citation type="doi">10.1093/bib/bbs038</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r ac3bae00a350 test-data/hg38.chrM.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg38.chrM.fasta Mon Aug 26 17:34:26 2024 +0000 |
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| b'@@ -0,0 +1,333 @@\n+>hg38.chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT\n+TTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTG\n+GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATC\n+CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTA\n+AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT\n+GTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCA\n+AACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTT\n+TATCTTTTGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATT\n+ATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCCGC\n+CCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCA\n+ACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAA\n+GCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAAT\n+AGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGA\n+ACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCAC\n+ACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTT\n+AACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGC\n+GGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTA\n+GATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACT\n+CCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCC\n+TAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAGC\n+CACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGG\n+AGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTC\n+AGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAA\n+GCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTG\n+GCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGC\n+TTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTC\n+AAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGA\n+GGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAA\n+CCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCA\n+ACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCACCT\n+TACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATG\n+AAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCT\n+GCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGA\n+CCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGT\n+CTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTAC\n+CGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTTTA\n+AATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGT\n+AAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAA\n+GCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACTGA\n+ACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATG\n+TTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGA\n+TTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCAAC\n+AAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTA\n+CCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCCCA\n+GTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCANNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTAAT\n+GCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGT\n+ACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCC\n+AATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCT\n+ATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCA\n+GGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATT\n+AAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCT\n+ATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATT\n+ATACCCACACCCACCCAAGAACAGGGTTTNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAAT\n+CGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATAC\n+AACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCC\n+TTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCG\n+CTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTC\n+AACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTC\n+AATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCG\n+CACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATC\n+ATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCT\n+TATCACAACACAAGAA'..b'CTTAGTTACCGCTAACAACCTATTC\n+CAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCAT\n+CAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAA\n+TCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATGA\n+TTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAG\n+GCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAA\n+GGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGC\n+AGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCAC\n+TAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCA\n+GCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTC\n+CACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATA\n+CTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGA\n+TATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACCT\n+CCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGT\n+TTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAA\n+CGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCT\n+ATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAA\n+ACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAACA\n+TTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACTC\n+ACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAA\n+CTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATT\n+TCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCCC\n+TATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCT\n+CCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTTC\n+CTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACC\n+TATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTT\n+CAACCAGTAACTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGC\n+ACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATTA\n+TTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAAC\n+ACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAA\n+TAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAA\n+ATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAAT\n+AACACACCCGACCACACCGCTAACAATCAATACTAAACCCCCATAAATAG\n+GAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACTC\n+AACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGA\n+CCCCAATACGCAAAACTAACCCCCTAATAAAATTAATTAACCACTCATTC\n+ATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCTC\n+ACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAG\n+CCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCAC\n+ATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCAA\n+TGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATC\n+CTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGTG\n+AGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCCG\n+CCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTAC\n+TCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTT\n+GCCCTTCATTATTGCAGCCCTAGCAACACTCCACCTCCTATTCTTGCACG\n+AAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTT\n+CCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGCG\n+ACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACATC\n+AAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCC\n+TAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAG\n+CAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGC\n+CCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGAC\n+AAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAACT\n+ATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTAT\n+AAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGG\n+ACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAG\n+ATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGT\n+ACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCAC\n+CTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTA\n+CAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC\n+CAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAA\n+CAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAA\n+ATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGAC\n+CACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACAT\n+CTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCT\n+TAAATAAGACATCACGATG\n' 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| diff -r 000000000000 -r ac3bae00a350 test-data/hg38.chrM.mm39.chrM.axt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg38.chrM.mm39.chrM.axt Mon Aug 26 17:34:26 2024 +0000 |
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| b'@@ -0,0 +1,4 @@\n+0 hg38.chrM 577 16569 mm39.chrM 1 15860 + 662318\n+GTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAA---TCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGT----TTTAGATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTT--GACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC-AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCT----CAGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCA-CGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCT-ACCCCAGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATA---GAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACAC-AAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACT--TGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCA------CCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAA-GTATAGGCGATAGAAATTGAAACCT---GGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAA----AATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATA-GAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACA-------CCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAA--TTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAAC--ATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAA-CAGCCCAATATCTACAATCA----ACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTA-CCCCGCCTGTTTACCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTAATGCAAACAGT--ACCTAACAAACCCACAGGTCCTAAACTACCA-AACCTGCATTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCGAACT-ACTATACTCAATTGATCCA---ATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCTATTCTAGAGTCCATATCAACAAT-AGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAA---GCGCCTTC--CCCCGTAAATGA-TATCATCTCAACTTAGTATTATACCCACACCCAC---CCAAGAACAGGGTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGACGCACTCTCCCCTGAACTCTACACAACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCTAGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCCTTATTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACC'..b'TCACATGATCAATTATACAATTCTCTTCATGATATATACACTCAGACCCAAACATCAATCGATTCATTAAATATCTTACACTATTCCTGATTACCATGCTTATCCTCACCTCAGCCAACAACATATTTCAACTTTTCATTGGCTGAGAAGGGGTGGGAATTATATCTTTCCTACTAATTGGATGATGGTACGGACGAACAGACGCAAATACTGCAGCCCTACAAGCAATCCTCTATAACCGCATCGGAGACATCGGATTCATTTTAGCTATAGTTTGATTTTCCCTAAACATAAACTCATGAGAACTTCAACAGATTATATTCTCCAACAACAACGACAATCTAATTCCACTTATAGGCCTATTAATCGCAGCTACAGGAAAATCAGCACAATTTGGCCTCCACCCATGACTACCATCAGCAATAGAAGGCCCTACACCAGTTTCAGCACTACTACACTCAAGTACAATAGTAGTTGCAGGAATTTTCCTACTGGTCCGATTCCACCCCCTCACGACTAATAATAACTTTATTTTAACAACTATACTTTGCCTCGGAGCCCTAACCACATTATTTACAGCTATTTGTGCTCTCACCCAAAACGACATCAAAAAAATCATTGCCTTCTCTACATCAAGCCAACTAGGCCTGATAATAGTGACGCTAGGAATAAACCAACCACACCTAGCATTCCTACACATCTGTACCCACGCATTCTTCAAAGCTATACTCTTTATATGCTCTGGCTCAATCATTCATAGCCTGGCAGACGAACAAGACATCCGAAAAATAGGAAACATCACAAAAATCATACCATTCACATCATCATGCCTAGTAATCGGAAGCCTCGCCCTCACAGGAATACCATTCCTAACAGGGTTCTACTCAAAAGACCTAATTATTGAAGCAATTAATACCTGCAACACCAACGCCTGAGCCCTACTAATTACACTAATCGCCACTTCTATAACAGCTATGTACAGCATACGAATCATTTACTTCGTAACAATAACAAAACCGCGTTTTCCCCCCCTAATCTCCATTAACGAAAATGACCCAGACCTCATAAACCCAATCAAACGCCTAGCATTCGGAAGCATCTTTGCAGGATTTGTCATCTCATATAATATTCCACCAAC--CAGCATTCCAGTCCTCACAATACCATGATTTTTAAAAACCACAGCCCTAATTATTTCAGTATTAGGATTCCTAATCGCACTAGAACTAAACAACCTAACCATAAAACTATCAATAAATAAAGCAA-ATCCATATTCATCCTTCTCAACTTTACTGGGGTTTTTCCCATCTATTATTCACCGCATTACACCCATAAAATCTCTCAACCT------AAGCCTAAAAACATCCCTAACTCTCCTAGACTTGATCTGGTTAGAAAAAACCATCCCAAAATCCACCT--------CAACTCTTCACACAAACATAACCACTTTAACAACCAACCAAAAAGGCTTAATTAAATTGTACTTTATATC------ATTCCTAATTAACATCATCTTAATTATTATCTTATACTCAATTAATCTCGAGTAATCTCGATAATAATAAAAATACCCGCAAACAAAGATCACCCAGCTACTACCATCATTCAAGTAGCACAACTATATATTGCCGCTACCCCAATC-CCTCCTTCCAACATAACTCCAACATCATCAACCTCATACATCAACCAATCTCCCAAACCATCAAGATTAATTACTCCAACTTCATCATAATAATTAAGCACACAAATTAAAAA---AACCTCTATAATCACCCCCAATACTAAAAAAC---CCAAAA--TTAATCAGTTAGATCCCCAAGTCTCTGGATATTCCTCAGTAGCTATAGCAGTCGTATATCCAAACACAACCAACATCCCCCCTAAATAAATTAAAAAAACTATTAAACCTAAAAACGATCCACCAAACCCTAAAACCATTAAACAACCAACAAACCCACTAACAATTAAACCTAAACCTCCATAAATAGGTGAAGGCTTTAATGCTAACCCAAGACAACCAACCAAAAATAATGAACTTAAAACAAAAATATAATTATTCATTATTTCTACACAGCATTCAACTGCGACCAATGACATGAAAAATCATCGTTGTAATTCAACTACAGAAACACCTAATGACAAACATACGAAAAACACACCCATTATTTAAAATTATTAACCACTCATTCATTGACCTACCTGCCCCATCCAACATTTCATCATGATGAAACTTTGGGTCCCTTCTAGGAGTCTGCCTAATAGTCCAAATCATTACAGGTCTTTTCTTAGCCATACACTACACATCAGATACAATAACAGCCTTTTCATCAGTAACACACATTTGTCGAGACGTAAATTACGGGTGACTAATCCGATATATACACGCAAACGGAGCCTCAATATTTTTTATTTGCTTATTCCTTCATGTCGGACGAGGCTTATATTATGGATCATATACATTTATAGAAACCTGAAACATTGGAGTACTTCTACTGTTCGCAGTCATAGCCACAGCATTTATAGGCTACGTCCTTCCATGAGGACAAATATCATTCTGAGGTGCCACAGTTATTACAAACCTCCTATCAGCCATCCCATATATTGGAACAACCCTAGTCGAATGAATTTGAGGGGGCTTCTCAGTAGACAAAGCCACCTTGACCCGATTCTTCGCTTTCCACTTCATCTTACCATTTATTATCGCGGCCCTAGCAATCGTTCACCTCCTCTTCCTCCACGAAACAGGATCAAACAACCCAACAGGATTAAACTCAGATGCAGATAAAATTCCATTTCACCCCTACTATACAATCAAAGATATCCTAGGTATCCTAATCATATTCTTAATTCTCATAACCCTAGTATTATTTTTCCCAGACATACTAGGAGACCCAGACAACTACATACCAGCTAATCCACTAAACACCCCACCCCATATTAAACCCGAATGATATTTCCTATTTGCATACGCCATTCTACGCTCAATCCCCAATAAACTAGGAGGTGTCCTAGCCTTAATCTTATCTATCCTAATTTTAGCCCTAATACCTTTCCTTCATACCTCAAAGCAACGAAGCCTAATATTCCGCCCAATCACACAAATTTTGTACTGAATCCTAGTAGCCAACCTACTTATCTTAACCTGAATTGGGGGCCAACCAGTAGAACACCCATTTATTATCATTGGCCAACTAGCCTCCATCTCATACTTCTCAATCATCTTAATTCTTATACCA---ATCTCAGGAATTATCGAAGACAAAATACTAAAATTATATCCATGTCTTGATAGTATAAAC-ATTACTCTGGTCTTGTAAACCTGAAATGAAGATCTTCTCTTCTCAAGAC--ATCAAGAAGAAGGAGCTACTCCCCACCACCAGCACCCAAAGCTGGTATTCTAA-TTAAACTA----------CTTCTTGAGTACATAAATTTACATAGTACAACAGTA----------CAT---------TTATGTATATCGTACATTA---------------------------------AACTATTT--------------------------------------------TCCCCAAGCATATAAGCTAGTACATTAAATCAATGGTTCAGGTCATAAAATAATCATCAACATAAATCAATATAT-----------ATACCATGAATATTATCTTAAACACATTAAAC------TAATGTTATAAGGACATATCTGTGTTATCTGACATA-CACCATACAGTCATAAACTCTTCTCTTCCATATGACTATCCCCTTCCCCATTTGGTCTATTAATCTACCATCCTCCGTGAAACCAACAACCCGCCCACCAATGCCCCTCTTCTCGCTCCGGGCCCATTAAACTTGGGGGTAGCTAAACTGAAACTTTATCAGACATCTGGTTCTTACTTCAGGGCCATCAAATGCGTTATCGCCCATACGTTCCCCTTAAATAAGACATCTCGATG\n+\n' |
| b |
| diff -r 000000000000 -r ac3bae00a350 test-data/hg38.chrM.mm39.chrM.chain --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg38.chrM.mm39.chrM.chain Mon Aug 26 17:34:26 2024 +0000 |
| b |
| @@ -0,0 +1,151 @@ +##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91 +##gapPenalties=axtChain O=400 E=30 +chain 673687 hg38.chrM 16569 + 576 16569 mm39.chrM 16299 + 0 15860 1 +19 2 0 +30 1 0 +92 1 0 +11 0 3 +41 2 0 +89 2 0 +80 0 4 +12 7 0 +41 0 2 +114 0 1 +129 0 4 +34 1 0 +29 0 1 +60 0 1 +39 1 0 +118 3 0 +14 0 3 +71 0 1 +31 3 0 +5 0 2 +39 0 6 +16 5 0 +23 0 1 +25 0 3 +37 0 4 +18 4 0 +206 0 1 +37 1 0 +56 2 0 +36 0 7 +84 2 0 +16 0 2 +57 0 2 +7 1 0 +30 2 0 +12 0 1 +20 0 4 +50 1 0 +42 0 1 +272 0 2 +25 2 0 +4 0 1 +74 1 0 +17 0 1 +19 0 3 +72 0 1 +139 1 0 +36 1 0 +10 0 3 +8 0 2 +12 0 1 +19 1 0 +14 0 3 +11 4 0 +1033 1 0 +189 0 1 +271 1 0 +22 1 0 +11 0 2 +83 0 1 +12 1 0 +280 0 3 +19 5 0 +11 0 2 +8 0 3 +14 3 0 +300 3 0 +11 3 0 +17 1 0 +50 6 0 +71 0 1 +56 2 0 +38 0 1 +73 0 3 +16 0 2 +33 1 0 +17 11 0 +1635 0 1 +32 0 1 +15 0 1 +683 22 0 +18 2 0 +26 2 0 +13 1 0 +101 1 0 +7 0 1 +26 0 9 +16 9 0 +1794 0 4 +7 1 0 +10 3 0 +77 0 3 +52 0 3 +13 0 1 +159 0 5 +13 5 0 +165 0 5 +8 5 0 +195 2 0 +7 0 2 +1155 1 0 +80 1 0 +139 1 0 +20 1 0 +23 0 1 +4 0 1 +1307 2 0 +13 0 2 +110 1 0 +10 0 1 +54 0 6 +11 6 0 +68 8 0 +13 0 2 +16 0 6 +33 6 0 +43 0 1 +103 1 0 +23 0 1 +89 3 0 +19 0 3 +10 3 0 +6 2 0 +9 0 2 +323 0 1 +1102 3 0 +12 0 3 +22 0 3 +20 1 0 +35 0 2 +12 2 0 +53 1 0 +8 10 0 +36 10 0 +3 9 0 +19 33 0 +8 44 0 +75 11 0 +6 0 5 +21 6 0 +5 0 1 +11 0 7 +12 1 0 +13 0 1 +136 0 1 +37 0 1 +47 + |
| b |
| diff -r 000000000000 -r ac3bae00a350 test-data/mm39.chrM.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mm39.chrM.fasta Mon Aug 26 17:34:26 2024 +0000 |
| b |
| b'@@ -0,0 +1,327 @@\n+>mm39.chrM\n+GTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAAATGCTTAGATGGAT\n+AATTGTATCCCATAAACACAAAGGTTTGGTCCTGGCCTTATAATTAATTA\n+GAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAAAATCCCTTA\n+AACATTTACTTAAAATTTAAGGAGAGGGTATCAAGCACATTAAAATAGCT\n+TAAGACACCTTGCCTAGCCACACCCCCACGGGACTCAGCAGTGATAAATA\n+TTAAGCAATAAACGAAAGTTTGACTAAGTTATACCTCTTAGGGTTGGTAA\n+ATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAATTATCTT\n+CGGCGTAAAACGTGTCAACTATAAATAAATAAATAGAATTAAAATCCAAC\n+TTATATGTGAAAATTCATTGTTAGGACCTAAACTCAATAACGAAAGTAAT\n+TCTAGTCATTTATAATACACGACAGCTAAGACCCAAACTGGGATTAGATA\n+CCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACAAAACTAT\n+TTGCCAGAGAACTACTAGCCATAGCTTAAAACTCAAAGGACTTGGCGGTA\n+CTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCT\n+ACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAA\n+CCCTAAAAAGGTATTAAAGTAAGCAAAAGAATCAAACATAAAAACGTTAG\n+GTCAAGGTGTAGCCAATGAAATGGGAAGAAATGGGCTACATTTTCTTATA\n+AAAGAACATTACTATACCCTTTATGAAACTAAAGGACTAAGGAGGATTTA\n+GTAGTAAATTAAGAATAGAGAGCTTAATTGAATTGAGCAATGAAGTACGC\n+ACACACCGCCCGTCACCCTCCTCNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNCTAGACATCCGTTTATGAGAGGAGATAAGTCGTAACAAGGTAAGCAT\n+ACTGGAAAGTGTGCTTGGAATAATCATAGTGTAGCTTAATATTAAAGCAT\n+CTGGCCTACACCCAGAAGATTTCATGACCAATGAACACTCTGAACTAATC\n+CTAGCCCTAGCCCTACACAAATATAATTATACTATTATATAAATCAAAAC\n+ATTTATCCTACTAAAAGTATTGGAGAAAGAAATTCGTACATCTAGGAGCT\n+ATAGAACTAGTACCGCAAGGGAAAGATGAAAGACTAATTAAAAGTAAGAA\n+CAAGCAAAGATTAAACCTTGTACCTTTTGCATAATGAACTAACTAGAAAA\n+CTTCTAACTAAAAGAATTACAGCTAGAAACCCCGAAACCAAACGAGCTAC\n+CTAAAAACAATTTTATGAATCAACTCGTCTATGTGGCAAAATAGTGAGAA\n+GATTTTTAGGTAGAGGTGAAAAGCCTAACGAGCTTGGTGATAGCTGGTTA\n+CCCAAAAAATGAATTTAAGTTCAATTTTAAACTTGCTAAAAAAACAACAA\n+AATCAAAAAGTAAGTTTAGATTATAGCCAAAAGAGGGACAGCTCTTCTGG\n+AACGGAAAAAACCTTTAATAGTGAATAATTAACAAAACAGCTTTTAACCA\n+TTGTAGGCCTAAAAGCAGCCACCAATAAAGAAAGCGTTCAAGCTCAACAT\n+AAAATTTCAATTAATTCCATAATTTACACCAACTTCCTAAACTTAAAATT\n+GGGTTAATCTATAACTTTATAGATGCAACACTGTTAGTATGAGTAACAAG\n+AATTCCAATTCTCCAGGCATACGCGTATAACAACTCGGATAACCATTGTT\n+AGTTAATCAGACTATAGGCAATAATCACACTATAAATAATCCACCTATAA\n+CTTCTCTGTTAACCCAACACCGGAATGCCTAAAGGAAAGATCCAAAAAGA\n+TAAAAGGAACTCGGCAAACAAGAACCCCGCCTGTTTACCAAAAACATCAC\n+CTCTAGCATTACAAGTATTAGAGGCACTGCCTGCCCAGTGACTAAAGTTT\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNATTATATAACTTATCTATTTAAT\n+TTATTAAACCTAATGGCCCAAAAACTATAGTATAAGTTTGAAATTTCGGT\n+TGGGGTGACCTCGGAGAATAAAAAATCCTCCGAATGATTATAACCTAGAC\n+TTACAAGTCAAAGTAAAATCAACATATCTTATTGACCCAGATATATTTTG\n+ATCAACGGACCAAGTTACCCTAGGGATAACAGCGCAATCCTATTTAAGAG\n+TTCATATCGACAATTAGGGTTTACGACCTCGATGTTGGATCAGGACATCC\n+CAATGGTGTAGAAGCTATTAATGGTTCGTTTGTTCAACGATTAAAGTCCT\n+ACGTGATCTGAGTTCAGACCGGAGCAATCCAGGTCGGTTTCTATCTATTT\n+ACGATTTCTCCCAGTACGAAAGGACAAGAGAAATAGAGCCACCTTACAAA\n+TAAGCGCTCTCAACTTAATTTATGAATAAAATCTAAATAAAATATATACG\n+TACACCCTCTAACCTAGAGAAGGTTATTAGGGTGGCAGAGCCAGGAAATT\n+GCGTAAGACTTAAAACCTTGTTCCCAGAGGTTCAAATCCTCTCCCTAATA\n+GTGTTCTTTATTAATATCCTAACACTCCTCGTCCCCATTCTAATCGCCAT\n+AGCCTTCCTAACATTAGTAGAACGCAAAATCTTAGGGTACATACAACTAC\n+GAAAAGGCCCTAACATTGTTGGTCCATACGGCATTTTACAACCATTTGCA\n+GACGCCATAAAATTATTTATAAAAGAACCAATACGCCCTTTAACAACCTC\n+TATATCCTTATTTATTATTGCACCTACCCTATCACTCACACTAGCATTAA\n+GTCTATGAGTTCCCCTACCAATACCACACCCATTAATTAATTTAAACCTA\n+GGGATTTTATTTATTTTAGCAACATCTAGCCTATCAGTTTACTCCATTCT\n+ATGATCAGGATGAGCCTCAAACTCCAAATACTCACTATTCGGAGCTTTAC\n+GAGCCGTAGCCCAAACAATTTCATATGAAGTAACCATAGCTATTATCCTT\n+TTATCAGTTCTATTAATAAATGGATCCTACTCTCTACAAACACTTATTAC\n+AACCCAAGAACACATATGATTACTTCTGCCAGCCTGACCCATAGCCATAA\n+TATGATTTATCTCAACCCTAGCAGAAACAAACCGGGCCCCCTTCGACCTG\n+ACAGAAGGAGAATCAGAATTAGTATCAGGGTTTAACGTAGAATACGCAGC\n+CGGCCCATTCGCGTTATTCTTTATAGCAGAGTACACTAACATTATTCTAA\n+TAAACGCCCTAACAACTATTATCTTCCTAGGACCCCTATACTATATCAAT\n+TTACCAGAACTCTACTCAACTAACTTCATAATAGAAGCTCTACTACTATC\n+ATCAACATTCCTATGGATCCGAGCATCTTATCCACGCTTCCGTTACGATC\n+AACTTATACATCTTCTATGAAAAAACTTTCTACCCCTAACACTAGCATTA\n+TGTATGTGACATATTTCTTTACCAATTTTTACAGCGGGAGTACCACCATA\n+CATATAGAAATATGTCTGATAAAAGAATTACTTTGATAGAGTAAATTATA\n+GAGGTTCAAGCCCTCTTATTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNN'..b'AAGGCCCTACACCAGTTTCAGCACTACTACACTCAAGTACAATAGTA\n+GTTGCAGGAATTTTCCTACTGGTCCGATTCCACCCCCTCACGACTAATAA\n+TAACTTTATTTTAACAACTATACTTTGCCTCGGAGCCCTAACCACATTAT\n+TTACAGCTATTTGTGCTCTCACCCAAAACGACATCAAAAAAATCATTGCC\n+TTCTCTACATCAAGCCAACTAGGCCTGATAATAGTGACGCTAGGAATAAA\n+CCAACCACACCTAGCATTCCTACACATCTGTACCCACGCATTCTTCAAAG\n+CTATACTCTTTATATGCTCTGGCTCAATCATTCATAGCCTGGCAGACGAA\n+CAAGACATCCGAAAAATAGGAAACATCACAAAAATCATACCATTCACATC\n+ATCATGCCTAGTAATCGGAAGCCTCGCCCTCACAGGAATACCATTCCTAA\n+CAGGGTTCTACTCAAAAGACCTAATTATTGAAGCAATTAATACCTGCAAC\n+ACCAACGCCTGAGCCCTACTAATTACACTAATCGCCACTTCTATAACAGC\n+TATGTACAGCATACGAATCATTTACTTCGTAACAATAACAAAACCGCGTT\n+TTCCCCCCCTAATCTCCATTAACGAAAATGACCCAGACCTCATAAACCCA\n+ATCAAACGCCTAGCATTCGGAAGCATCTTTGCAGGATTTGTCATCTCATA\n+TAATATTCCACCAACCAGCATTCCAGTCCTCACAATACCATGATTTTTAA\n+AAACCACAGCCCTAATTATTTCAGTATTAGGATTCCTAATCGCACTAGAA\n+CTAAACAACCTAACCATAAAACTATCAATAAATAAAGCAAATCCATATTC\n+ATCCTTCTCAACTTTACTGGGGTTTTTCCCATCTATTATTCACCGCATTA\n+CACCCATAAAATCTCTCAACCTAAGCCTAAAAACATCCCTAACTCTCCTA\n+GACTTGATCTGGTTAGAAAAAACCATCCCAAAATCCACCTCAACTCTTCA\n+CACAAACATAACCACTTTAACAACCAACCAAAAAGGCTTAATTAAATTGT\n+ACTTTATATCATTCCTAATTAACATCATCTTAATTATTATCTTATACTCA\n+ATTAATCTCGAGTAATCTCGATAATAATAAAAATACCCGCAAACAAAGAT\n+CACCCAGCTACTACCATCATTCAAGTAGCACAACTATATATTGCCGCTAC\n+CCCAATCCCTCCTTCCAACATAACTCCAACATCATCAACCTCATACATCA\n+ACCAATCTCCCAAACCATCAAGATTAATTACTCCAACTTCATCATAATAA\n+TTAAGCACACAAATTAAAAAAACCTCTATAATCACCCCCAATACTAAAAA\n+ACCCAAAATTAATCAGTTAGATCCCCAAGTCTCTGGATATTCCTCAGTAG\n+CTATAGCAGTCGTATATCCAAACACAACCAACATCCCCCCTAAATAAATT\n+AAAAAAACTATTAAACCTAAAAACGATCCACCAAACCCTAAAACCATTAA\n+ACAACCAACAAACCCACTAACAATTAAACCTAAACCTCCATAAATAGGTG\n+AAGGCTTTAATGCTAACCCAAGACAACCAACCAAAAATAATGAACTTAAA\n+ACAAAAATATAATTATTCATTATTTCTACACAGCATTCAACTGCGACCAA\n+TGACATGAAAAATCATCGTTGTAATTCAACTACAGAAACACCTAATGACA\n+AACATACGAAAAACACACCCATTATTTAAAATTATTAACCACTCATTCAT\n+TGACCTACCTGCCCCATCCAACATTTCATCATGATGAAACTTTGGGTCCC\n+TTCTAGGAGTCTGCCTAATAGTCCAAATCATTACAGGTCTTTTCTTAGCC\n+ATACACTACACATCAGATACAATAACAGCCTTTTCATCAGTAACACACAT\n+TTGTCGAGACGTAAATTACGGGTGACTAATCCGATATATACACGCAAACG\n+GAGCCTCAATATTTTTTATTTGCTTATTCCTTCATGTCGGACGAGGCTTA\n+TATTATGGATCATATACATTTATAGAAACCTGAAACATTGGAGTACTTCT\n+ACTGTTCGCAGTCATAGCCACAGCATTTATAGGCTACGTCCTTCCATGAG\n+GACAAATATCATTCTGAGGTGCCACAGTTATTACAAACCTCCTATCAGCC\n+ATCCCATATATTGGAACAACCCTAGTCGAATGAATTTGAGGGGGCTTCTC\n+AGTAGACAAAGCCACCTTGACCCGATTCTTCGCTTTCCACTTCATCTTAC\n+CATTTATTATCGCGGCCCTAGCAATCGTTCACCTCCTCTTCCTCCACGAA\n+ACAGGATCAAACAACCCAACAGGATTAAACTCAGATGCAGATAAAATTCC\n+ATTTCACCCCTACTATACAATCAAAGATATCCTAGGTATCCTAATCATAT\n+TCTTAATTCTCATAACCCTAGTATTATTTTTCCCAGACATACTAGGAGAC\n+CCAGACAACTACATACCAGCTAATCCACTAAACACCCCACCCCATATTAA\n+ACCCGAATGATATTTCCTATTTGCATACGCCATTCTACGCTCAATCCCCA\n+ATAAACTAGGAGGTGTCCTAGCCTTAATCTTATCTATCCTAATTTTAGCC\n+CTAATACCTTTCCTTCATACCTCAAAGCAACGAAGCCTAATATTCCGCCC\n+AATCACACAAATTTTGTACTGAATCCTAGTAGCCAACCTACTTATCTTAA\n+CCTGAATTGGGGGCCAACCAGTAGAACACCCATTTATTATCATTGGCCAA\n+CTAGCCTCCATCTCATACTTCTCAATCATCTTAATTCTTATACCAATCTC\n+AGGAATTATCGAAGACAAAATACTAAAATTATATCCATGTCTTGATAGTA\n+TAAACATTACTCTGGTCTTGTAAACCTGAAATGAAGATCTTCTCTTCTCA\n+AGACATCAAGAAGAAGGAGCTACTCCCCACCACCAGCACCCAAAGCTGGT\n+ATTCTAATTAAACTACTTCTTGAGTACATAAATTTACATAGTACAACAGT\n+ACATTTATGTATATCGTACATTAAACTATTTTCCCCAAGCATATAAGCTA\n+GTACATTAAATCAATGGTTCAGGTCATAAAATAATCATCAACATAAATCA\n+ATATATATACCATGAATATTATCTTAAACACATTAAACTAATGTTATAAG\n+GACATATCTGTGTTATCTGACATACACCATACAGTCATAAACTCTTCTCT\n+TCCATATGACTATCCCCTTCCCCATTTGGTCTATTAATCTACCATCCTCC\n+GTGAAACCAACAACCCGCCCACCAATGCCCCTCTTCTCGCTCCGGGCCCA\n+TTAAACTTGGGGGTAGCTAAACTGAAACTTTATCAGACATCTGGTTCTTA\n+CTTCAGGGCCATCAAATGCGTTATCGCCCATACGTTCCCCTTAAATAAGA\n+CATCTCGATGGTATCGGGTCTAATCAGCCCATGACCAACATAACTGTGGT\n+GTCATGCATTTGGTATCTTTTTATTTTGGCCTACTTTCATCAACATAGCC\n+GTCAAGGCATGAAAGGACAGCACACAGTCTAGACGCACCTACGGTGAAGA\n+ATCATTAGTCCGCAAAACCCAATCACCTAAGGCTAATTATTCATGCTTGT\n+TAGACATAAATGCTACTCAATACCAAATTTTAACTCTCCAAACCCCCCAC\n+CCCCTCCTCTTAATGCCAAACCCCAAAAACACTAAGAACTTGAAAGACAT\n+ATAATATTAACTATCAAACCCTATGTCCTGATCAATTCTAGTAGTTCCCA\n+AAATATGACTTATATTTTAGTACTTGTAAAAATTTTACAAAATCATGTTC\n+CGTGAACCAAAACTCTAATCATACTCTATTACGCAATAAACATTAACAA\n' 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