diff --git a/probes/mapping/blast/1_primers.fasta b/probes/mapping/blast/1_primers.fasta deleted file mode 100644 index cf92a71823f4873ae96e8fd294283fc4348b8eaf..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/1_primers.fasta +++ /dev/null @@ -1,13 +0,0 @@ ->JBPP0904F_primer -ACGCTCGCCTTCTTCATTACC ->JBPP0904R_primer -GTGTCCCGAAGGCTAAGCAC ->JBPPH036P06F_primer -CCCTTGTTAGTGGGTATGTTGGC ->JBPPH036P06R_primer -AGTGGCTTGTTGGGTGGTTAG ->JBSC0201F_primer -CCCTTGTTAGTGGGTATGTTGGC ->JBSC0201R_primer -AGTGGCTTGTTGGGTGGTTAG - diff --git a/probes/mapping/blast/2_sequences.fasta b/probes/mapping/blast/2_sequences.fasta deleted file mode 100644 index e50f0e88a8d8ae97e13300f94da473854e3a3a25..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/2_sequences.fasta +++ /dev/null @@ -1,100 +0,0 @@ ->JBPP0904F -AGCACTTTTCTACACAATTGTGGTTTCATGCGCCCCGAATACTTTAACAGCGATAAAAAAGTGCATTGTTGATGCNCGCT -GATTTNTGTAAATTTGAAAACTATAGAAAGAACTGAGTTACCTGAATGAAATCTAGACGATTTGATGTACTGTCCATCTC -CGTGTCCAACTCACTTAAGATCTTCTCCTGCAAGAACATATATTGATTTTAACTACATTTTGCTTCGGAGGAGTTTAAGC -AGAGCTGCAATTTGTTCAGTGACAAATTCAAGGAACTGGTTAAGCAGGTGGTCGCACTCACGTGTGCAAGAAGTTCATCG -TGTATGGTGAGCCCAACATCTCCAATTCTGACTACGCTGGCACTAAGCTCGTCTAGTTCTTCATCCTGTTGCCTGCACAG -ACGATCAAGAAAATACGCTTTCTGAAAGTTATACTTAAAAGCTATAAAAATGACATAGTACCATATCAAATAGATTCAAG -ATTATGCTACATCCTCTAAATTCTACGTTAATTGAAGTCTTCTCGACATAATTTAAGTGCTGGCAAAACTATACTGCTAA -TACCTTTAATAACAGGTACTAAAGGGTATTCAATACAGCATACTATTCCATGATAAATGAAGTTAAGTAGACAAACTCAG -AAAGCTAAAAAGACATGGCAGAATGGTTATGACTATGACATAAAGATCTTAGAGAGGCTGATGATACATATTATCCTCCC -CTTATAAATAAAATCAAAGGCTAGGATTCCATAGTAAAGATTGAGAAAACATTAAGATGCCTCAGAAAGATAAATGGATA -GGTGCATGCAAGATTTACAGTGAGATCGGAATAAAAATCAATTGGTAATAAAAATGACAAACAAGGATAGATGCAAAGAA -ATGGAGGGNAATATTACCCTCATAAGAAGTAATNGTCTATCTGNATNCTGATGATATGAAGTCANCATTNATCNCGGGCA -TNGTATGCATTGGGATCNCNCCTTNCCNGTNCANAANCNTGGGCAATCTCAACAGGNNCTCGCCGGNATCCCACNNCAGA -ATTANANGGTACNTGGNCCCCNTTGGACTGGTNNNCCNCC - ->JBPP0904R -CANTATGNATTAAAGTTTTGTGAATCATGCTTTCTTNCCATACGAATTCTGTACAAATGATTTGAATTTCTAAAAAAGCN -ATAAACTAATGTTGAGTTGAATGCATCAAGGAGCTCATTAGATTGCCGATTTGGCTATATAAATGCCCAAATATATACTG -CACATCGGCCTTTTAATGGATATCAGCACAGGTTTGTGGTCTATTTCAAGCTACTCTCACCCTGGTCTATTCCCATGAAA -TCATGTGCCATGTTCCTCACTGTCATTCACATTTTTTTTCTTGTTTCGTGAAATGAAAGACACAAACCTATGTCTTTCCA -TTTATCAAAAGAGGATCAGTTTAGTTTGAATTTTGTGAGTTCAATTGGATTGGGATGGAATTTATCTACGAAAAGCTTAC -TTTCCAAAATTTTGACAAATCTCATTTTGTATGGGGATTTCCACAGGACCCTTTTCCTTTGTTAAGAGTTATATTTTGTT -CTCATCTCATGGATAAATGTTTCTTATCTAAAAAGAGAACTTTGAGTTCTTTGCTTTACCTGAAAAACCAACAATTCATA -TTCGAAAGGTTTAGAATGGCAATCTGGAACTCTTGTAGCAATAACAACTACCATTACAAACCTGAAGGGTAACATGGACT -TGTTAAGGTTTGATTCAGTTGGGTTTCTTTGCGTTTTTTCTCATTTCTCAGACGAGTTAGTTGTAGAAGACAGGTTGTTC -ACCTTATTTACTATAGGACTGTTAGCATTTGCACTTCTCCATTAGCTTTTAAGTATTTTAGGTTCAGCCCAGACCAAAAG -TGTTCACTTTGAACAAACATAAAGGCACATTTATGCTTAGCGTTATATATCAACAAGCAAAATACTCCTAACTCTTTTCT -GACGGGAGTCCGGGGACAATTTTGGAGTTTTNGCACTNGATATTNGTAATGCCTTCCTACTGGAGATAATATCATTGGGN -CATGTATAGGAGTATNATNNNNCTGGGAATCACCCTTCNGGGTAATNNNCATATTNNCTCGGNAAAANCCCCTTNTNGGC -TAAAGN - ->JBPPH036P06F -CAACCTATCCTTTCTGGCTTGGTGCTTTCTCCTGCCCCCAGTCTATTGTGTGCTTTTATTGCAGTTGCAAGATATGCANC -CTGCCACTCCNATGCCACCATCCATACTCAGCCGTGGCGTAGGTTGGCAGGTAAACAGATGCTGCCCCCCTGTAAACTCC -CCTCCCTAGCCCAACTTTCTAATACAATGACTTGAAAGGGAAAACGCAAACTTANNCGTTATGTTATGGAATTCGAACGC -AGAATCAAATACATAGGGTGGTTTGAAAGGNTTATATGGAGAGTCATGACATTGTTNNCAGTCTGCCCAGATNAGCCTTT -GCCANCAGAAGATTCCTNCAGCTCATACCCCAAAAGTTCTTCAGCTAGTACCCCAAGTCGGGCACATACATGGCNCTGGA -AATATTNANTTAGGGGACGTGGNNGGNGGTGGANGANAAGGGCNCGTNNACCNGGNCGANGANCNGAAGAANANCAACAA -AGNNCAANTAACTCANGACCAGACCGCCTCTTCAAAAATGAAAATGTCGGACNGGTATCAAGCTGNNGNAAAATANTGCT -ANACCCACCNNCCATGTGGGTGAACAGGNCCGCAACNAGCAAGCACNGTGNGGCANTGGAAATACNGCGGNCGGATAAGC -CCANCANCANGNAAGAACCTACTGTATCTGGGTAACGGAAGCTATAAANCTNGCCAACNGAAAAAGATGGTAAGCCNCCA -GCCCCNNAAANNACAAAGANACCCTCTACCACACAAAANNCCCGCGNTAACAGTGNANNCCCCNTTTAGGCGANNAANNA -ACGTTNNNCGGNGGNNCCTNCCCAGNGNNTTTANGAANCNNCACCCAGGGNTAAAACGAAANAANNCNCCCCAAAANANG -NGGGGGCANNNCCACNNGGGTCCCAGGGNAATCNGNGGNTCNAANANACNNGGCCCCCCATNGNNNCCCCCCCGGNANAA -AGAAAAACNAANCCCCCCNNCCCNNANANNNCCCCNCAANTATGGCAANGCNNAANGGCAACCCCNGAGNGGGNGGNNAA -TNAAANGNTTNNNCCNCGGNNNAAAGANAAAAAAAANAACNGGNNGGGCNNGCCCATNCNGGGCACNTNCCGNNNNGCGC -CAACGNGACACCANATTTTNGCCAAAGGNGCACCTCNCCNCNAAANNGCGGNCCTNAATNACAACCCGCGCGCGNNNNGG -GGNTCAGCGGCACAACAANAAAAANATTNTCNNNCNNGGGGGGGACAAACNCCCCCGTTGGTGTGTTATAAA - ->JBPPH036P06R -NANTGACGACTAGGAACNCCAAAGGTTGCTATATTGCCCCTCAAATCTTTATATCCATGAATTTACAACAGAAAAATAAN -CCACTAAGTANTCTTCAAAATGGTCAGACTAGTTATACTTTCCTTTCTTTTGCATACATATAAAAGAAAATATGTGTAGC -AGAAGTGAGGCCCCAATGAAGAATTCATTGACAAGGGGTTTTATCGTGTATGAACCGTTTTGTTTTGTTCCTCAATATGA -TCTCATACTGACGGGAAATACTTGTTGAGATTGAACGGAAGAGAGTAGAATTCCTCACTTCTTGTGTCACTCTTGAAGGA -CCGGAACTTGTTCCACCACGGCTTGCCTCTGTCTTTCTTTGTCGAACTCTCCTTTTTGTGCATTGTATTGTCCAGGAAAT -AAGCCAATATGCCAGCAACAAAAGCTTCTGATGAGAAGGGCACGTTCACCATGTCGTTGAACTGAAGAATAACAACAAAG -CACAAGTAACTCTTTTCAGCCACCTCTCAAAAATGAAAATGTTAGACATGTATTAAGCTAGTGTTAATTATTGCTATACC -CATCGTCCATGTGTGTGAACAGGTCCGTAACCAGCAATCACAGTGTATTCATTGAAGTACTGCGGTACTGATAAACCCAA -AAAGATTGAAAAACCTAATATAAACTTGTTACGGAAACTATTAAGATTGCAGAACTGAAGAAAGCTTAAGCCTCCAACCC -CTACAAACAAAGAGAACAAGTAATCACTAACTCCTCATAACGTGANCCACATATTGGTAATGATCATCACACAGGGGNTN -CCCCTNGGNNTATTTACGTACCCNACATAAGCNAAGAATAGGCNATAGAGAGCGNCCTACNAANGGGGNGCTGGGAANTC -NAAGCCAAAGANGGCNCCCAAANTTTTNCCTGGAAAAANAAAANAAAAGNNGCCTNCNAGNANAAANTAACCNTGCCNAN -AAAAANGGAGCCTGGGGGGGGGGGNCGANAANTNTNCNGCCGAAAAAACCCAANAAAAAANNGTGNCCCCCCCCAAAATA -ANCTTGGGNCNGGNNNAAAATTNCCCCCNGNANNNGGNNNNNGNAAAANNCCTNNNCCCCCCCNCCGGGNTTTTNTGGNA -NCAAAACNCNNTNCNNGNCNGGGCCAANNCCCNNGGGTTNNNGGGGNNAAAAAAAAACCNNN - ->JBSC0201F -NCAACTAANCTTCTGGCTTGGTGCTTCTCCTGCCCCAGTCTATTNGTTGCTTTTATTGCAGTTGCAAGATATGCAACGTG -CCACTCCNATGCCACCATCCATACTCAGCCGTGGCGTAGGTTGGCAGGTAAACAGATGCTGCCCCCCTGTAAACTCCCCT -CCCTAGCCCAACTTTCTAATACAATGACTTGAAAGGGAAAACGCAAACTTTTTTGTTATTTTATTGAATTTGAACGCAGA -ATCAAATACATAGGGTGGTTTGAAAGGTTTATATGGAGAGTCATGACATTGTTTTCAGTCTTCCCAGATTAGCCTTTTCC -ACCAGAAGATTTCTTCAGCTCATACCCCAAAAGTTCTTCAGCTAGTACCCCAAGTCTGTCACATACATGCCTCTGTTTTT -ATTTATTTAGGGGAGGTGGGTGGGGGTGGGGTGTATATGGGCATATATGGAAAGANAANNAATNNGGAATNCTCAGNNNG -ATNCANNAGAAGAATGATNGTNCTNGCACNNCCTCATNCCGGNCTGNNACCAANATGNTCCANNATNATNATCATATGAN -GAANCNNNNNGNTGNATNNANNNNCCAAANNNNNGNNATGTNANGGAANNGGNATNNNANNGNNNNGNNNGNNCGGNNNN -GNGAANGGATNNNNNGNNTNNGNGNNNNNNNNNGNNANANNNNNNNNNNNNNNNNANGANGGNNNANANNNNNNNNNNNN -NANANNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNGNNNGNNNNNNNNNNNNNNNNANNNNNNGNNNNNNGNNNANNNN -NNNNNANNNNNNNNNNNGNNNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNN -NNNNNNNNNNGNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN -NNNNNNNNNNNNNNNNANNNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN -NNNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN - ->JBSC0201R -ANTGACGACTAGGAANCCAAAGTTGCTATATTGCCCCTCAAATCTTCATATCCATGAATTTACAACAGAAAAATAATCTA -CTAAGTANCTTCAAAATGGTCAGACTAGTTATACTTTCCTTTCTTTTGCATACATATAAAAGAAAATATGTGTAGCAGAA -GTGAGGCCCCAATGAAGAATTCATTGACAAGGGGTTTTATCGTGTATGAACCGTTTTGTTTTGTTCCTCAATATGATCTC -ATACTGACGGGAAATACTTGTTGAGATTGAACGGAAGAGAGTAGAATTCCTCACTTCTTGTGTCACTCTTGAAGGACCGG -AACTTGTTCCACCACGGCTTGCCTCTGTCTTTCTTTGTCGAACTCTCCTTTTTGTGCATTGTATTGTCCAGGAAATAAGC -CAATATGCCAGCAACAAAAGCTTCTGATGAGAAGGGCACGTTCACCATGTCGTTGAACTGAAGAATAACAACAAAGCACA -AGTAACTCTTTTCAGCCACCTCTCAAAAATGAAAATGTTAGACATGTATTAAGCTAGTGTTAATTATTGCTATACCCATC -GTCCATGTGTGTGAACAGGTCCGTAACCAGCAATCACAGTGTATTCATTGAAGTACTGCGGTACTGATAAACCCAAAAAG -ATTGAAAAACCTAATATAAACTTGTTACGGAAACTATTAAGATTGCAGAACTGAAGAAAGCTTAAGCCTCCAACCCCTAC -AAACAAAGAGAACAAGTAANCACTAACTCCTCATAACGTGAACCACATATNGGNAATGATCATCACNCAGGGGCTNCCCC -TNGTNTATNNACGTNCCCTACCNTANNCNANNGAATAGGCNANNNNAGAGGCGCCCTACCNNNGGGGTGGNNGGGNNTCN -NANNNNNANNACGGGNNCCCNANNNNNNCCTGGNAANANNAANNAAANGGGCNNTNNNNNATNANNNAACCNNGNCNNNN -NNANNNNNNNNGGGGNGNGGGGGGNNANNNNNNNNNNNNGNNNNNNNNNNNNAAANNNNNGNNNCNNNCNNNNNNNNNNN -NNNGNNNCNGGGGGNNNNNNCCCCNNNGGNNNNNGGNNNNNNNNNNNNNCNNNNNNCCCCNNNGCNNGGNNNNNNNNGNN -NNCNNNNNNNCNNNNNNNNNNNGNNCNNNNNNNNNNNGNNN - diff --git a/probes/mapping/blast/JBPP0904_Product.fasta b/probes/mapping/blast/JBPP0904_Product.fasta deleted file mode 100644 index e776c0645602c0bd141e2bd77a9ad743feae65ec..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/JBPP0904_Product.fasta +++ /dev/null @@ -1,61 +0,0 @@ ->S_lycopersicum_chromosomes.fa_SL2.40ch12_62702453_62706035_JBPP0904_Product -ACGCTCGCCTTCTTCATTACCATGCCAATCTTTTTCTACAACAAATTGTGGTTTCCATGC -GATAAGAATACAATAACAGCGATAAAAAAGTGCATTGTTGATGCGGCTGATTTAGTAAAT -TTGAAAACTATAGAAAGAACTGAGTTACCTGAATGAAATCTAGACGATTTGATGTACTGT -CCATCTCCGTGTCCAACTCACTTAAGATCTTCTCCTGCAAGAACATATATTGATTTTAAC -TACATTTTGCTTCGGAGGAGTTTAAGCAGAGCTGCAATTTGTTCAGTGACAAATTCAAGG -AACTGGTTAAGCAGGTGGTCGCACTCACGTGTGCAAGAAGTTCATCGTGTATGGTGAGCC -CAACATCTCCAATTCTGACTACGCTGGCACTAAGCTCGTCTAGTTCTTCATCCTGTTGCC -TGCACAGACGATCAAGAAAATACGCTTTCTGAAAGTTATACTTAAAAGCTATAAAAATGA -CATAGTACCATATCAAATAGATTCAAGATTATGCTACATCCTCTAAATTCTACGTTAATT -GAAGTCTTCTCGACATAATTTAAGTGCTGGCAAAACTATACTGCTAATACCTTTAATAAC -AGGTACTAAAGGGTATTCAATACAGCATACTATTCCATGATAAATGAAGTTAAGTAGACA -AACTCAGAAAGCTAAAAAGACATGGCAGAATGGTTATGACTATGACATAAAGATCTTAGA -GAGGCTGATGATACATATTATCCTCCCCTTATAAATAAAATCAAAGGCTAGGATTCCATA -GTAAAGATTGAGAAAACATTAAGATGCCTCAGAAAGATAAATGGATAGGTGCATGCAAGA -TTTACAGTGAGATCGGAATAAAAATCAATTGGTAATAAAAATGACAAACAAGGATAGATG -CAAAGAAATGGAGGGAATATTACCTCATAAGAAGTAATTGTCTATCTGATTCTGATGATA -TGAAGTCATCATTATCTCGGGCATTGTATGCATTGGATCTCTCTTTCTGTTCAGAATCTG -GCAATCTCAACAGTTCTCGCCGCATCCCACTCAGATTAGATGTACTTGTCCCATTTGACT -GTTTTCCAGCTACTACAGCTTTCTTCATGCTTCCCACCTGGTTAAAGGCAATTTGAAATC -GTTTATTTATTTTCAGGAACCAAGAAACAAAAGAATAGATATTTGGCATCAACAGAATCA -GTTATACTTGAGCACGGGCATTGCTGGTCCATCTTCTTCTCTTATCAAGCTCAATATCAT -TAATACCATACCAAGAAGGATCTCTTGCTGCAACATCAATTGTTTTGTCCAATTCATCCA -CCTTCTCATCAAGAAAACAGGAATTCAGCATTGATAAGGATATGAAGCAAGTCATAGCAG -CAGTAGATCAATATCAAATCACACTGACAGAAGAACAACTCTGGTTATGTTGCTATTGTT -CACTGAAAGAAGAACATCTTTCCCTAAGTACTAAAGTCGACAGATTGGACAGCACAAATT -CATAGACTGAACTTAAGACAGGTGCAACACATCAAACATGCAATTGTCTCTGGCTATTCA -AAATTGTCGTAATTCATTCACGTAAAGTACAGGCAATCAGGAAGAAATATAATGAGAATT -TAACAGACCAAACAGTGATAAGTATCAATTAACCAAGTTTCAAGGAGCTACGTTTCCGCA -CATACCTGCCACTCAATGCTCTCAGATGAAGCAAGAAGTTCTTTGGTAAGATGTACTTGC -TCACTACTTCCGGCAGAAGTTTGCTCCCATTGATGAAACGTGGACAAGAGCTTGTCAATC -TAACCAAGCAGGAATTTCAAGAGTTAGATTAAGTAGTCAACAAACTTGATCACATATGAG -ATCCAACAGATTCTACCAGCAAGGAGAGTCTTAGCTTATTTTTTCTTAATAGTAAAAGAG -ATGAAATTTCTTAGTTTGTTCAGCTTGTTTTTTTATTTTTTCTATGAAAATAGACAATAG -CCACAAGAAAATCATAGCTTTCTTACCTGTTAGCTGTTACTGGAGTACTTGATTTTTAAA -CCTTAGTCTCGAAGAATTATACTTTATCTCATAGAAACATTACTCACCCCCTTCCCAGAA -TGTCGAGAGAGATGGAGATAGATACATGACAGGAAACACCACCAACCCTTCATGAATCTA -TCTCCCATGCAAGAATAAGAACAACACACTAATAAAAAAAAACAAATCTCAGACGAATAA -GATTTACTTCACTTCAAGATTATTAGAACATAACTAGATCGAAGTAGATGAACTTACAGA -TTCTTGAATTTCCTCCTTGACAATATAGAAAGGATCTTGAGCTGAAGACATCTTCAACAC -CAACTGTAGAACATTTAAGTGGACACATCAGATAATTAAATAACATATATAATACATATA -AAAAGCATCAGGAGAAAGATGATCGAGAACTATATCTTATACCCAGACATTGCAAAGTAG -TACATCTCAAAATGCCTTTTCCGTAAAGTGTATTATGACAGAGAGATACAGTGGCACTTT -AGCAAGAAGGGCTTTTCCGAGAAAATATGAAAATTACCAGAAGGATGAATTCCAAGAAAA -ATAATACTCCTATACATGACCAAATGATAATTATCTCCAGTAGGAAGGCATTACAAATAT -CAAGTGCAAAAACTCAAAATTGTCCCCGGACTCCCGTCAGAAAAGAGTTAGGAGTATTTT -GCTTGTTGATATATAACGCTAAGCATAAATGTGCCTTTATGTTTGTTCAAAGTGAACACT -TTTGGTCTGGGCTGAACCTAAAATACTTAAAAGCTAATGGAGAAGTGCAAATGCTAACAG -TCCTATAGTAAATAAGGTGAACAACCTGTCTTCTACAACTAACTCGTCTGAGAAATGAGA -AAAAACGCAAAGAAACCCAACTGAATCAAACCTTAACAAGTCCATGTTACCCTTCAGGTT -TGTAATGGTAGTTGTTATTGCTACAAGAGTTCCAGATTGCCATTCTAAACCTTTCGAATA -TGAATTGTTGGTTTTTCAGGTAAAGCAAAGAACTCAAAGTTCTCTTTTTAGATAAGAAAC -ATTTATCCATGAGATGAGAACAAAATATAACTCTTAACAAAGGAAAAGGGTCCTGTGGAA -ATCCCCATACAAAATGAGATTTGTCAAAATTTTGGAAAGTAAGCTTTTCGTAGATAAATT -CCATCCCAATCCAATTGAACTCACAAAATTCAAACTAAACTGATCCTCTTTTGATAAATG -GAAAGACATAGGTTTGTGTCTTTCATTTCACGAAACAAGAAAAAAAATGTGAATGACAGT -GAGGAACATGGCACATGATTTCATGGGAATAGACCAGGGTGAGAGTAGCTTGAAATAGAC -CACAAACCTGTGCTGATATCCATTAAAAGGCCGATGTGCAGTATATATTTGGGCATTTAT -ATAGCCAAATCGGCAATCTAATGAGCTCCTTGATGCATTCAACTCAACATTAGTTTATTG -CTTTTTTAGAAATTCAAATCATTTGTACATGGTTCGTATCCAAGAAAGCATGATTCACAA -AACTTTTAATTGACATTACTGAAGTGCTTAGCCTTCGGGACAC diff --git a/probes/mapping/blast/JBSC0201_Product.fasta b/probes/mapping/blast/JBSC0201_Product.fasta deleted file mode 100644 index 61b15f1744468ef391ec99918be091b4ade1d5de..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/JBSC0201_Product.fasta +++ /dev/null @@ -1,33 +0,0 @@ ->S_lycopersicum_chromosomes.fa_SL2.40ch12_16714760_16716664_JBSC0201_Product -CCCTTGTTAGTGGGTATGTTGGCCAAATCTAATCTCTTTCTTGCTTGTGCTTTCTCCTGT -TTCAGTCTACTGGTGCTTTTATTGCAGTTGCAAGATATGCAAGTGCCACTCCCATGCCAC -CATCCATACTCAGCCGTGGCGTAGGTTGGCAGGTAAACAGATGCTGCCCCCCTGTAAACT -CCCCTCCCTAGCCCAACTTTCTAATACAATGACTTGAAAGGGAAAACGCAAACTTTTTTG -TTATTTTATTGAATTTGAACGCAGAATCAAATACATAGGGTGGTTTGAAAGGTTTATATG -GAGAGTCATGACATTGTTTTCAGTCTTCCCAGATTAGCCTTTTCCACCAGAAGATTTCTT -CAGCTCATACCCCAAAAGTTCTTCAGCTAGTACCCCAAGTCTGTCACATACATGCCTCTG -TTTTTATTTATTTAGGGGAGGTGGGTGGGGGTGGGGTGTATATGGGCATATATGGAAAGA -CAATTAATTTGGAATTCTCAGTTTGATTCACGAGAAGAATGATTGTTCTTGCACTTCCTC -ATTCCGGTCTGTTACCAACATGCTCCATTATTATCATCATATGACGAACCTTTTTGCTGT -ATTTACTTTCCAAATTCTTGTTATGTCAGGGAATTGGCATTTTACTGTCGGGTTTGTTCG -GCACCGGGAATGGATCTTCTGTATCTGTGTAAGTACAGGCGAAATCTTCTTCAGCACAAT -AGGATGGTAGAAATTAGTTATCTAAGACGAATTAACTCTCTTCATACACATGCAGTGAAA -ATGCTGGTCTTTTAGCACTAACACGTGTTGGCAGCCGAAGAGTTGTTCAGATATCAGCAG -GGTTTATGATTTTCTTTTCAATTCTTGGTAATTTTCCTGTCCAAGTATTTTGTTGAGTAA -ATTTTCTTGATTTTCGCTGATATTTTATCCCTCCCCAGCTCCTCTTTTGCATGTTATTTA -TCTAAATGCACTTTGTTTCTTTTCAGGAAAATTTGGTGCCGTCTTTGCTTCGATTCCAGC -ACCCATTGTAGGCGCTCTCTATTGCCTATTCTTTGCTTATGTAGGTACGTAAATATACAA -GGGAAGCCCTGTGTGATGATCATTACCAATATGTGGTTCACGTTATGAGGAGTTAGTGAT -TACTTGTTCTCTTTGTTTGTAGGGGTTGGAGGCTTAAGCTTTCTTCAGTTCTGCAATCTT -AATAGTTTCCGTAACAAGTTTATATTAGGTTTTTCAATCTTTTTGGGTTTATCAGTACCG -CAGTACTTCAATGAATACACTGTGATTGCTGGTTACGGACCTGTTCACACACATGGACGA -TGGGTATAGCAATAATTAACACTAGCTTAATACATGTCTAACATTTTCATTTTTGAGAGG -TGGCTGAAAAGAGTTACTTGTGCTTTGTTGTTATTCTTCAGTTCAACGACATGGTGAACG -TGCCCTTCTCATCAGAAGCTTTTGTTGCTGGCATATTGGCTTATTTCCTGGACAATACAA -TGCACAAAAAGGAGAGTTCGACAAAGAAAGACAGAGGCAAGCCGTGGTGGAACAAGTTCC -GGTCCTTCAAGAGTGACACAAGAAGTGAGGAATTCTACTCTCTTCCGTTCAATCTCAACA -AGTATTTCCCGTCAGTATGAGATCATATTGAGGAACAAAACAAAACGGTTCATACACGAT -AAAACCCCTTGTCAATGAATTCTTCATTGGGGCCTCACTTCTGCTACACATATTTTCTTT -TATATGTATGCAAAAGAAAGGAAAGTATAACTAGTCTGACCATTTTGAAGTTACTTAGTA -AATTATTTTTCTGTTGTAAATTCATGGATATGTGGATTTGAGTAGCAATATAGCAACTTT -GGTGTTTCCTAGTCGTTGCAAAATCTAACCACCCAACAAGCCACT diff --git a/probes/mapping/blast/blast2align.pl b/probes/mapping/blast/blast2align.pl deleted file mode 100755 index 2b740789bd852783a44fbb9c293fe418f439fc83..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/blast2align.pl +++ /dev/null @@ -1,236 +0,0 @@ -#!/usr/bin/perl -w -use strict; - - -my $inFile = $ARGV[0]; -die if ! defined $inFile; -die if ! -f $inFile; - -my %res; - -&readFile($inFile); -&printRes(); - -sub printRes() { - my $matrix = &getSubMatrix(); - #$res{$lastQuery}{seq } = \@seq; - open COV, ">$inFile.cov" or die; - my $totalScore = 0; - - foreach my $qry ( sort keys %res ) { - my $data = $res{$qry}; - my $start = $data->{start}; - my $end = $data->{end }; - my $len = $end - $start + 1; - my $seq = $data->{seq }; - my $seqLen = scalar @$seq; - - print "query $qry\n"; - print " START $start END $end LEN $len SEQLEN $seqLen\n"; - my $title = "$qry $start "; - my $ref; - my $cov; - - for ( my $p = 0 ; $p < $seqLen; $p++ ) { - my $nuc = $seq->[$p]; - #print "NUC $nuc\n"; - - if ( ! defined $nuc ) { - $ref .= "-"; - $cov .= "0"; - print COV ($p+1), "\t0\n"; - } else { - my $refNuc = uc(substr($nuc, 0, 1)); - my $covNum = length($nuc ) -1; - my $covLen = length($nuc ); - $ref .= $refNuc; - my $score = 0; - my $lMatrix = $matrix->{$refNuc}; - - for ( my $n = 1 ; $n < $covLen ; $n++ ) { - my $lNuc = uc(substr($nuc, $n, 1)); - my $lScore = $lMatrix->{$lNuc}; - $score += $lScore; - #print " FROM $nuc COMPARING $refNuc WITH $lNuc SCORE $lScore ( $score - $n - $covNum )\n"; - #if ( $nuc eq $refNuc ) { - # $score += 1; - #} - #elsif ( $nuc eq "-" ) { - # $score += 0; - #} - #else { - # $score += -0.5; - #} - } - - $cov .= $score . ","; - $totalScore += $score; - print COV ($p+1),"\t",$score,"\n"; - } - } - - print "$title TOTAL SCORE $totalScore\n"; - if ( 0 ) { - my @ref = split(//, $ref); - my @cov = split(/,/, $cov); - #my $ref = $title; - #my $cov = " "x(length($title)); - - for ( my $q = 0; $q < @ref; $q+=30 ) { - my $r = $q + 30; - if ( $r > @ref ) { - $r = @ref - 1; - } - my $rf = ""; - my $co = ""; - for ( my $s = $q; $s < $r; $s++ ) { - $rf .= sprintf("%4s ", $ref[$s] ); - $co .= sprintf("%4s ", $cov[$s] ); - } - print "$rf\n$co\n"; - } - } - } - close COV; -} - - -#sub getSubMatrix { -# #http://guinevere.otago.ac.nz/aef/MLRGD/usersguide/node18.html -# # T C A G -# my @matrix = -# ( -# ( -1, .6, .2, .2 ), -# ( .6, -1, .2, .2 ), -# ( .2, .2, -1, .6 ), -# ( .2, .2, .6, -1 ) -# ); -# # extend open -# my @gap = ( -1, -3); -#} -sub getSubMatrix { - #http://guinevere.otago.ac.nz/aef/MLRGD/usersguide/node18.html - # T C A G - my %matrix = - ( A => { A => 1.0, C => -1.0, G => 0.5, T=> -1.0, '-' => -2.0 }, - C => { A => -1.0, C => 1.0, G => -1.0, T=> 0.5, '-' => -2.0 }, - G => { A => 0.5, C => -1.0, G => 1.0, T=> -1.0, '-' => -2.0 }, - T => { A => -1.0, C => 0.5, G => -1.0, T=> 1.0, '-' => -2.0 }, - '-' => { A => -2.0, C => -2.0, G => -2.0, T=> -2.0, '-' => 1.0 }, - ); - return \%matrix; -} - -sub readFile { - #Query= S_lycopersicum_chromosomes.fa_SL2.40ch12_62702453_62706035_JBPP - #0904_Product - # (3583 letters) - - #Database: tomato - # 13 sequences; 781,666,411 total letters - - #Searching..................................................done - - - - # Score E - #Sequences producing significant alignments: (bits) Value - - #SL2.40ch12 6747 0.0 - - #1_0 1 acgctcgccttcttcattaccatgccaatctttttctacaacaaattgtggtttccatgc 60 - #12 62702453 acgctcgccttcttcattaccatgccaatctttttctacaacaaattgtggtttccatgc 62702512 - - #1_0 61 gataagaatacaataacagcgataaaaaagtgcattgttgatgcggctgatttagtaaat 120 - #12 62702513 gataagaatacaataacagcgataaaaaagtgcattgttgatgcggctgatttagtaaat 62702572 - - - my $infile = shift; - - open IN, "<$infile" or die; - - my $lastQuery = ""; - - while (my $l = <IN>) { - chomp $l; - #print "L $l\n"; - - if ( $l =~ /^Query= (.+)/ ) { - $lastQuery = $1; - print "QUERY $lastQuery\n"; - - while ( my $m = <IN> ) { - chomp $m; - #print "M: $m\n"; - if ( $m =~ /\((\d+) letters\)/ ) { - print "SIZE $1\n"; - $res{$lastQuery}{size} = $1; - last; - } - elsif ($m =~ /Length\=(\d+)$/ ) { - #Length=1089 - print "SIZE $1\n"; - $res{$lastQuery}{size} = $1; - last; - } - $lastQuery .= $m; - } - #print "end query\n"; - - my $hspLen = 0; - while ( my $n = <IN> ) { - chomp $n; - #print "N: $n\n"; - - if ( $n =~ /^((?:\d+|Query)_\d+)\s+(\d+)(\s+)([acgt\-\s]+)\s(\d+)/i ) { - #printf "NAME %4s START %010d END %010d SEQ '%s'\n", $1, $2, $5, $4; - my $hspName = $1; - my $hspStart = $2; - my $hspSpacing = $3; - my $hspSeq = $4; - my $hspEnd = $5; - my $hspTab = length($hspStart) + length($hspSpacing); - - $res{$lastQuery}{start} = $hspStart if ! exists $res{$lastQuery}{start} || $hspStart < $res{$lastQuery}{start}; - $res{$lastQuery}{end } = $hspEnd if ! exists $res{$lastQuery}{end } || $hspEnd > $res{$lastQuery}{end } ; - my @seq = split(//, $hspSeq); - $hspLen += scalar @seq; - - while ( my $o = <IN> ) { - chomp $o; - if ( $o =~ /^(\d+)\s+(\d+)(\s+)([acgt\-\s]+)\s(\d+)/i ) { - #printf " HIT CHR %4s START %010d END %010d SEQ '%s'\n", $1, $2, $5, $4; - - my $hitName = $1; - my $hitStart = $2; - my $hitSpacing = $3; - my $hitSeq = $4; - my $hitEnd = $5; - my $hitLen = $hitEnd - $hitStart; - - my $hitTab = length($hitStart) + length($hitSpacing); - my $hitTabDiff = "."x($hitTab - $hspTab); - $hitSeq = $hitTabDiff . $hitSeq; - - #print " HSP SPACING '$hspSpacing' HSP TAB LEN $hspTab HIT SPACING '$hitSpacing' HIT TAB LEN $hitTab HIT TAB DIFF '$hitTabDiff'\n"; - - my @hitSeq = split(//, $hitSeq); - for ( my $i = 0; $i < @hitSeq; $i++ ) { - my $hitChar = $hitSeq[$i]; - if ( $hitChar =~ /[acgt-]/i ) { - $seq[$i] .= $hitChar; - } - } - } else { - last; - } # if $hit - } # while my $o - #print " PUSHING ", scalar @seq, " ($hspLen)\n"; - @{$res{$lastQuery}{seq }}[$hspStart-1..$hspEnd-1] = @seq; - } # if 1_0 (reference) - last if $n =~ /Posted date\:/; - } # while my $n - } # if qry - } # while my $l (qry) - close IN; -} diff --git a/probes/mapping/blast/ch12-sc02-1_Product.fasta b/probes/mapping/blast/ch12-sc02-1_Product.fasta deleted file mode 100644 index aa3f2355f9f801f6c6dfe7f3b9d9d2f8621deab0..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/ch12-sc02-1_Product.fasta +++ /dev/null @@ -1,33 +0,0 @@ ->S_lycopersicum_scaffolds.fa_SL2.40sc04878_622710_624594_ch12-sc02-1_Product -TCCCTTGTTAGTGGGTATGTTGGCCAAATCTAATCTCTTTCTTGCTTGTGCTTTCTCCTG -TTTCAGTCTACTGGTGCTTTTATTGCAGTTGCAAGATATGCAAGTGCCACTCCCATGCCA -CCATCCATACTCAGCCGTGGCGTAGGTTGGCAGGTAAACAGATGCTGCCCCCCTGTAAAC -TCCCCTCCCTAGCCCAACTTTCTAATACAATGACTTGAAAGGGAAAACGCAAACTTTTTT -GTTATTTTATTGAATTTGAACGCAGAATCAAATACATAGGGTGGTTTGAAAGGTTTATAT -GGAGAGTCATGACATTGTTTTCAGTCTTCCCAGATTAGCCTTTTCCACCAGAAGATTTCT -TCAGCTCATACCCCAAAAGTTCTTCAGCTAGTACCCCAAGTCTGTCACATACATGCCTCT -GTTTTTATTTATTTAGGGGAGGTGGGTGGGGGTGGGGTGTATATGGGCATATATGGAAAG -ACAATTAATTTGGAATTCTCAGTTTGATTCACGAGAAGAATGATTGTTCTTGCACTTCCT -CATTCCGGTCTGTTACCAACATGCTCCATTATTATCATCATATGACGAACCTTTTTGCTG -TATTTACTTTCCAAATTCTTGTTATGTCAGGGAATTGGCATTTTACTGTCGGGTTTGTTC -GGCACCGGGAATGGATCTTCTGTATCTGTGTAAGTACAGGCGAAATCTTCTTCAGCACAA -TAGGATGGTAGAAATTAGTTATCTAAGACGAATTAACTCTCTTCATACACATGCAGTGAA -AATGCTGGTCTTTTAGCACTAACACGTGTTGGCAGCCGAAGAGTTGTTCAGATATCAGCA -GGGTTTATGATTTTCTTTTCAATTCTTGGTAATTTTCCTGTCCAAGTATTTTGTTGAGTA -AATTTTCTTGATTTTCGCTGATATTTTATCCCTCCCCAGCTCCTCTTTTGCATGTTATTT -ATCTAAATGCACTTTGTTTCTTTTCAGGAAAATTTGGTGCCGTCTTTGCTTCGATTCCAG -CACCCATTGTAGGCGCTCTCTATTGCCTATTCTTTGCTTATGTAGGTACGTAAATATACA -AGGGAAGCCCTGTGTGATGATCATTACCAATATGTGGTTCACGTTATGAGGAGTTAGTGA -TTACTTGTTCTCTTTGTTTGTAGGGGTTGGAGGCTTAAGCTTTCTTCAGTTCTGCAATCT -TAATAGTTTCCGTAACAAGTTTATATTAGGTTTTTCAATCTTTTTGGGTTTATCAGTACC -GCAGTACTTCAATGAATACACTGTGATTGCTGGTTACGGACCTGTTCACACACATGGACG -ATGGGTATAGCAATAATTAACACTAGCTTAATACATGTCTAACATTTTCATTTTTGAGAG -GTGGCTGAAAAGAGTTACTTGTGCTTTGTTGTTATTCTTCAGTTCAACGACATGGTGAAC -GTGCCCTTCTCATCAGAAGCTTTTGTTGCTGGCATATTGGCTTATTTCCTGGACAATACA -ATGCACAAAAAGGAGAGTTCGACAAAGAAAGACAGAGGCAAGCCGTGGTGGAACAAGTTC -CGGTCCTTCAAGAGTGACACAAGAAGTGAGGAATTCTACTCTCTTCCGTTCAATCTCAAC -AAGTATTTCCCGTCAGTATGAGATCATATTGAGGAACAAAACAAAACGGTTCATACACGA -TAAAACCCCTTGTCAATGAATTCTTCATTGGGGCCTCACTTCTGCTACACATATTTTCTT -TTATATGTATGCAAAAGAAAGGAAAGTATAACTAGTCTGACCATTTTGAAGTTACTTAGT -AAATTATTTTTCTGTTGTAAATTCATGGATATGTGGATTTGAGTAGCAATATAGCAACTT -TGGTGTTTCCTAGTCGTTGCAAAAT diff --git a/probes/mapping/blast/ch12-sc02-2_Product.fasta b/probes/mapping/blast/ch12-sc02-2_Product.fasta deleted file mode 100644 index ef6fbd0db552c7c5c373e6ec869d6615ecf68420..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/ch12-sc02-2_Product.fasta +++ /dev/null @@ -1,32 +0,0 @@ ->S_lycopersicum_scaffolds.fa_SL2.40sc04878_3080728_3082538_ch12-sc02-2_Product -AAGAACTCTCTTCGGGTGGAGTAATTATACTACCATATGAAACAACAATTGAACTCTTTG -ATGGAATGGTTAAGACCAACAAGCAGATAGGAAAATATCAAAAACTTGATACATAACTGA -CTCAGCTGGATATTTTGGCCAAGAAAGTCAATAAATTGAAGGCAATGTACAAAAAGAACA -ACAAATACGTTTCCCCTCACAAGCATAGAATTTCCAATGAAATATGAGGGTAGACAGGAT -GATCAGAACATCTTACTTATTTATCCCAATGTCATGGAACACGAAAGAGTGTTAAAAAAG -ATAAAGAGAGAATTTCTTGATGATGAATTAGATGACAACCTCTTATTCCATGTTCACTGA -TCTTGTAGAGTCCCAAATGGACAAGGTGTTGTCTAGTCTCTATCCAAAGCATAGAAAAGG -GTTTACTAATGAGAATGTGGAAAACCCCAATAATGAAATCTAAGTGGAGACTTGCACCAT -GCAACAATGTTAACTAAGGAGAATAATGGGAGGCAAACAAAGTTTTATAGATTTATTTTA -TAGAAAAATCGTGTGATAATTTTGTATGTTAAACTGTAGAATTTGTTAAAAGGTACAGGT -TGGCGACCCAAATTTCTACTTGGCGACTCACCAAAGAGGTCGGTGATCCCAACTTGGACC -GTTGTTGCACTCAAGAAATTCTAAAGCTGGAGTCTATAAAACTTCGTATGCCCATGAGCA -AATCAGCGTGTTGTCAAGCAGGTCGTCAACCATTAATTTGACCGCCGTTTGGGCCCTTAC -TAACTGAAGGTCATGTAGCACTCGACGAGGTAATGTCTCACTTGGTGTGTCGCCGAATGG -GGGGATGAGAAAAATTAATGCCGCCGTCGCCGAACGGGCGAGAACTATATGGTTTTAAGG -TCCAAAAGTTTAAAAGTCAAAAACCATTCAGATTCCCTTACTTTTGGATTTCCCAAACTT -GCACCCATACTATATTTTCTATATTTTTGTGTTTCTACCACTCATTAGTAATCCATTGTG -TATTTGTAATTTGATACCATTGTGGCCTAGCATTTCAACTCATTTATTTTGCTTCTAAGG -TTGGTTTTCGAAGCCTTGAACTCATATCTAGAGATTTTATTCATTTAGATTTGTGTTGAT -ATTTGTGAAGTGTGCTAGGCCTCTCTGGCTTAATTGTTTCTATTATTGTATGCTTATTTC -AATAACTTAATTTGGTGATCTCGCCTAAAATTATTTAATGTTGATTTATGGAAATTCTCA -TGCTTATGTTTGATCAACATTATTTGGTTATGATATTTTCTTGTTGGGTCAAGTCAGGTG -ATGTCTAAGAATCCAACATTTGTGTAAATGATGCACTTAGAGAAATGATGGAGCGATTAA -CGTGATTCCTAAAGGCCAAAGTCATTAAATTGATAGATTTTGTTAAACTTGTAGAAGTCT -AAGTATCCTAGGATCATGTGTAGCGTTGCTCTAAGTCTAATTGAATGAGTTCATTGTTTT -ATTTGGTTTTTTGGGGCTGCAGGGTTGTATTTCTGAAGTTAGGGTTGAGATTAGGTATGT -TAGGTCATTTGAAGAGCTGAGCCGAGCTCGCCGAACCACTTAGTGGTTTGCCAAATCCCC -CCTAATCGTCTTTCACATCAAGCAAAGTTTGAATTTTTGTGTTATAACATTCGGCGAGAA -GCCCGAGTTCACAAATTGCACTCAGATGCTCGCCAATTGTCATTTTTATCTCCCTTTTTT -CCCCCAACCCTTAAAAATGCATTGTATATTTTGGCGGGCTTGTCTTGCTCACCGAATGTT -TTCGGCAATTT diff --git a/probes/mapping/blast/ch12-sc02-3_Product.fasta b/probes/mapping/blast/ch12-sc02-3_Product.fasta deleted file mode 100644 index 1e8f845b14a25d128174dca09362f2af3f98b0c9..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/ch12-sc02-3_Product.fasta +++ /dev/null @@ -1,20 +0,0 @@ ->S_lycopersicum_scaffolds.fa_SL2.40sc04878_4093931_4095019_ch12-sc02-3_Product -AACCCTCAATACAAACATGAAAGTCACTTATTTCTACCATATTCATAGGATATCCCCCTA -TGCTATCCTCAACATTTAAAATAGAATTGAAGTCCTCCATTATTATCCATGGAAGCATGT -TACCTGCGTTCATATCATCTAAATATTTTCACAACTCTTTCCTTTCCTCTCGTGTGTTGA -AAGCATATACGACAGTTACAATATACTCCAAATTGAGGCTTTGATTTTGTATTTTACAGG -TTATCGCCTAGGCGCAACTTGCAACCATTAGCACTTGAAAGTAATCTGGCCTCCATGTTA -TCAATACCCCACTGTTATAATTGTCGACAAGATTAGTAACATAGTCCAATCCTCCAAACG -AGCTTCTATCCACCCTGTCAATATTACTCATTTTGATCTTAGTCTCTATCAAATCCACAA -ATCCAGTACTTTCTTTACTACAAAGGAGTTTTATCTCCTTTTGTTTGTTAAGAGTGGTTA -AACCCCTATAGTTCCATCACATCATGCTATCCATTCATGCTGGGAGTCGCTGTCCCTCCC -CCATTTATAGTTGTGGCCGTTGAAGGTTGTTCTTTCACTTCTTCTGTATGTAGAACCTGA -AACGTGTTCTTACGATCCACCTCTCCCTGATGAACATGCTTCTTCTGCCTATTTGGACTT -AATGACTTAGTCATTGGAGTGATCCACCCTGCTGTCCTTCCTCCTTGTACAGTTGTATCT -GTTCCAGTTTTTTCGGCTCCATCAATGACCCTATGGTTTATCATTTCAGTTTGTCTTCCT -CTGTATTGATTGTATGTCCCTCTTTATTTTTGCTTCCCTTTGTCTTTCACTATGTTTGGT -TGTTACTCTTCTCCTTTCCTTTGATCCGGAGGTGGGTTTTTCTTCGTGCAAATCCCTTCA -TCATGTCCATACTTTTTTCAAAAATTACACAGTATGGGCTTCCAATCGTACTGCACTTTT -TGTTCAATCAGCTCTCCTCTCTTATTTTTGAAGAAAACTTTATCCGGTAGTTCTGCTTTT -ATTCCACTTCTATCAGTAGCCTGACAAAACTGTGTCCTAATTTCTTTTCTGTGTTTTGGT -CCACCATTA diff --git a/probes/mapping/blast/ch12-sc03-1_Product.fasta b/probes/mapping/blast/ch12-sc03-1_Product.fasta deleted file mode 100644 index af7c750e203631463cd2209d979932be145162c3..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/ch12-sc03-1_Product.fasta +++ /dev/null @@ -1,43 +0,0 @@ ->S_lycopersicum_scaffolds.fa_SL2.40sc04057_3198454_3200936_ch12-sc03-1_Product -TAGGAAGCAAAGGTAGTTTGGGATGAGTAGGAAGTACAACTAAGGATAATACACAATGAT -TGGGAAGTTTTCAAATGGATAGCCAGACATCCAAGAGTTTAGGAAATTAATACCAAAACA -ATGGGGTTTGAAAGGGGAAGTAAATATTGGGTTATTAAGTAGCAAATATGTATTGATAAG -GGTCTCACTACCAGAAGATTATGTGAACTTATTATCAAAAACTCAATTTTATATCGGTTG -TAACAATTCGTCGTACTCAATGAGAACCATGAAATAGGACCTTTGTTTGATGAAAAGGAG -GAAATGACTACAACGATAGTTTGGATCTCTTTTCCATCACTGCCACCAAACCTTTTTGGT -AAGGAGACAATCTTCTAATAGTTGCAACAATATCAAGACTATTACAGGCATACATGGAAA -CTCAAAACAAAACAATACCAAGTTTTTCAAGGGTAAAGATAGAGGTGAATCTTTTAGGGG -AATGACCCAAAAGAAACAATATTAACATGAGGAAAAAGAACACTGAAGTTATGAAAAAAT -GGGTGACCATTCAATATAATTATATTCCAAAGTATTGTATAACTTGCAAGCTTCATGGGC -GTAATGAGAAGGAGTGCTATCTTATATATTATGAACTTTTCACACAAATGGAACAGACGG -AGGAGGGAGAAAAGGTGCAAGTTAATAAGGAAGACAAGGGCGTTAAAGTAAATCAACAAG -CAAAGAAAGGGACGAAGTGAAAAAACCAAGATCATTTTTATAAAGGTAAAGAGGAAAATA -AAAAGATAGCTAAAGAAAATGTTTTTACTGAGTAGGGAAGAAGGAATGGGTACAGAAGGT -GGTATAATTATGAAAAAATATAACCAGAACAAGTCTGGAATAAAAGAGTACAAGAAGCGA -AAAAAGCAGAAGTGAATACAGTGAACAAATTTGAGGATTTAGAAGATACATTACCTGGAC -AAGAGGATAACAATGAGGTAGAAAGAATGGAAAATAAGGATACAGACATTTAGAAGAGGT -TTGAAGACAAGGTACAAGGGAAAGAATGAGATACTGTTAACTTCAGTTGCCATAGGGAGA -ACAAAAAAAAGTTCTGACCGAAGTATAATATTTTATAGCCCGGAAACCTCTATTGTGAAA -GATACAAGTATCATTTCTAGTGTGGAAGTAACACAATAGGAGAATGAGAGAAACAATGGA -GGGTAATGGAGAAAACACTAACAAAGGAACAACAAGTTGTGTTAAATTTGAAACAAGCAA -AAAATTGTCGTAATTAAAAGATAGACAAGCATAGCCCAGGAGAGTTACATGATAAACATG -ATACAGAGGAGGAAGAGATCCTAGAATCTCACATACAGGAGACATGAAGAGAAGGAGACT -TATTCCCTCAACAAATAAAAAAATTGAATGGAAAATATTGGGAAAGAAGGAACAACATTC -GAGATATGACTTATGTAACCACAAAACCCAAAATGATCAGCCCCTCCATATTCATGTATG -ATTAGTAAAGTGCTATTTTGGACCATTAGGTTGGTAAAATCTCAAAATTCTTTTGAAAGG -CTACTAGACCTAAATAGGAAAATCATTAGGCATACATTGCTCTTTTCCATCCTTCTAAAG -TCCATCGACTAGAAAAGCAACAATCCAAAGTTAATTTGTCTTTCAAATTTTGGTTGTTTT -GGGATGAGAAGTGGGAAGGGAAAGTTGTTTTGACACACTGCATGAAATTACAATCACTCT -AAAGCATGGAGACAACAATGGTGTTGTCAAAATTACAACAATTATGCTAGATGTAGTGCC -TTGGAGATATTTAAATTGTGTAAAGACCTTGTGGTGGTTTTTAACAATACACATTTTACA -TGGATGGGAAGGGGAGATTTCAATACCATAATAGATGAGTCAGAAAAGATGGGAGGTCTG -CCAGTCTCGCAACTTGAAGTTGAAGATTTTGTTCAATGTATAAGTTCTTGGATATTGAAT -GTAATAAAATTCTCAAGAAACAAGTATACCTTATGGAATGGCATAACAGAGGCTGGCTAT -ATTTTTGAATGGTTGGATAGAGTCTTTGGGAGCAATGACCTCACGAAGGAGTTCTAAAAC -ACTGAAGTGAAACATTTGATTGGGGAGGGCTTAGACCATGACCCATTGCATAATACTTGA -AATGCATCACAAAAGCAGATTTACAAGCCTTTTTGGCTTAACTTCTAGGAAAAACAACAC -AACTTTCAACGTACAGCGGAAGATATTTGGAATATGGAGGAAATATGCTCCCCTTTTACA -GTAGTTTAAACAAAATTGGAAAGGGTGAAATCAGCTTTGGTCCAATGGAGCAAAAATACT -TTTGGACATATTTTTCAATAGGTGGAAAAAATAGAAGATGTACCATTTGTGATGAAAACT -TAATTTACATGGTTTAAATTGTATTTTATCCCCCATTTGAGTTTGAAATAGAGTAATTTG -AAGTCCTACGTGTTAGGAATTAT diff --git a/probes/mapping/blast/ch12-sc03-2_Product.fasta b/probes/mapping/blast/ch12-sc03-2_Product.fasta deleted file mode 100644 index 56ba122432225e2222bfe6ba65b9eaac1c66bc59..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/ch12-sc03-2_Product.fasta +++ /dev/null @@ -1,45 +0,0 @@ ->S_lycopersicum_scaffolds.fa_SL2.40sc04057_7835794_7838398_ch12-sc03-2_Product -GACCTGTCCCTTCCATACCTAAGTCATAAATTACCAAATGTACCAGTGGAAGTTGCAAAT -AAGGAAATTGGGTCCTAGAACTCAAAACGACCTACTGGGCCGTCACATATCATTGCCTTG -TAAAAAATTGAAAATGATCACTTCATGGTAGAACTTCGATCCGAGTTCCTCAAATTGTTC -TTTCACACTGACATTTTTATTTTCCTGGATAACTGTCACGAGGTTGGAGGTTTTTGTTCC -TTTTTCAATTTCTATGCATCCAATATTAACCTCCTATTTTTACAGGCTGAACATCCCACT -TTGTCAAATATTAATTTGGATATACCAGTTGGTGAGCTAGTTGCTATTGTGGGTGGGACT -GGAGAAGGAAAGACATCTCTGATTTCAGCAATTCTTGGGGAGTTTCCTCCTTTAGGCAAT -GCAAGTGTCACTATCAGAGGTTCCATTGCATATGTTCCTCAAGTTTCCTGGATCTTCAAT -GCCACTGTGAGCTTCAATTTATCCCTATTCCTTGTTATGCCTGTAGCACAAGTATGTTTA -CATGAGCATACTATTTCGGGGAGTCATTACAATATGTTGTAGATATTCTTAAAATGTGAT -AAATTATCTCTGGGTATTTATATGAAACAATGCAATTACCTTTACCTTACTGTTTTTAGG -TACGTGAAAATATATTATTTGGTTCCAACTTTGAACCAACAAGATATTGGAAGGCAATAA -ACGTCACTGCATTGGACCATGATCTTGAGTTACTTCCAGTTAAGTACATTTGATGGTAGT -GTATTTGTGTCAATATATCTTTATGATGTATGGAATTTTCTATTTACTAGTTAGTCTAAA -TGAAACTGCTATGTTCACACATATAAAATATTCAGGGTGGGGACCTTACAGAAATCGGCG -AAAGAGGAGTGAATATTAGCGGAGGACAAAGGCAAAGAGTGTCGATGGCTAGAGCTGTCT -ACAAAAATTCCGATATCTATATATTTGATGATCCCTTAAGTGCTCTTGATGCACATGTTT -CCCATCAGGTAATTATCTTGTATGAATGCCTGGACAACACCATTTCAGTAAGGGAATGGG -ATATCAACATTACCTGAGAAGACCTTCCTTCTATATCCAATCTTCATATCCACCACCTGT -AGATTTTTCCAAATTGACTAACCTCTTTCGTGTATATGTACAAGACTAATTTGCAGTAAT -TGGTCATAATTCACTGATTGCAATTGTTCCATCGTTCTTGTTGCAGTTTTTAAGCATATG -CTAAATTCAATTTGGATCTAACTTGCAGTGCAATGGGATTTTTCAGGTTTTTAAAAACTG -TATAAAGGAAGAATTGCAAGGAAAGACTAGGGTGCTTGTGACAAATCAGCTGCATTTTCT -ACCTCAGGTGGATCGGATCATTTTGGTTTCTGAAGGAATGGTGAAAGAGGATGGGACCTT -CGAGAAGCTTTTGGAACATGGCACACTTTTTCCAAAGCTAATGGAAAATGCTGGGAAAAT -GGAAAGTTATGGTGTTGAAACTGAATATGACCCAAACTTTGACAGTGAGAGTTCACAGTC -TTCAAGCACAAGGCAAGAGCACCAACAAGATGTAACCTCTGTAACCAAAAGGAAGGCTGG -TAAATCTGTTCTTATCAGGCAGGAAGAGCGGGAAACTGGTATTATCAACTGGAGTGTTTT -GATGAGGTAACAAGTTAATGTATATGCTTTGAGACATTTATCCTTGGAAATTTTAATCAA -GTCACTCAGACATGAATATCCTGGTAATTCAACAATTTTAGAATCCTAATTTCTTTTTCA -GAATTTTTAAAAAGACGAGACTTACAACATTTATTAAGAGAAAAATTCATGGCACAAACT -TTTCTCAAATATTTCCATTCTCTTGCTTCTCCCATTGCATCTAGACACTGGTGGAATTAA -AAAATGTTATTGTCTGTAGTGCATAGTTTCTAGCATGGGCCTTGGAATATTCCATTTATT -TCTAGTGGTTTGTGTACCCCCTTTAGGAACACAACATCATCGTTGAGGTTTTCCTAATCT -CCATACTAGGGGATGTGTCGGCTCCAATACCACCTGTAATAGCTAGGCCCCAACTGCCAA -GGTATTCCCTAACGCAACCTTTTAGTCCTTGCGGTTTTCTCCCCTTGTTACCCAAAGGCA -TCCCAGAATTGAATTCCTGACCTCGCTCTGTATAACCCCTAACTTTTTCCTCCAGTTCTG -ATGTGCTATTTATCTAAGGTAAGTGATAACAACAAGGTCAGGGAGATCGCAATTTTAGAG -TTTTGAGTACTGGACGTGCGGAAGAAAAATATGAATGAATCTGGAATATGAGAATAAAGA -TATTGGAATTCGACGGAACAGTCCACAAATTTCCATGAATGTGATGTTTTAAAGCTTTGA -CAAGGTCAAGAGTAACAAAATATTGATTATGAGAAGAAATATAACACCTTTGCTTGAGAA -AATGAATCAAAACGATAGATTTGGATCTTGTCCACTTCATGATAACTTAAACAACAATTA -GTATGGAAAAACTATTCGCCTTTTAAAGAATATCAAAAAGGAATCACTGATATCACAAGA -AGAAACTACCTTTACATCAAGACTT diff --git a/probes/mapping/blast/ch12-sc03-3_Product.fasta b/probes/mapping/blast/ch12-sc03-3_Product.fasta deleted file mode 100644 index db906257043031d5a2dce36ce28c89afa605f1b1..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/ch12-sc03-3_Product.fasta +++ /dev/null @@ -1,46 +0,0 @@ ->S_lycopersicum_scaffolds.fa_SL2.40sc04057_13401063_13403730_ch12-sc03-3_Product -AGCTCCCATGATTGTAGAGCATCCACATGTTTCTCCAGTCAAGAACTGCAAAACAACTCT -TTGCTAAGGCTGCTTGTACTACTAAAAATCTAGAATATTTTGGGTCAAGAGTGATATGCA -GGTGGTTGTGCCAAGTTGGAAGTGAGATCTGAGTGTTTGTATAATTGTGCTTGCAGGGGT -GGTTTACATGATGTTGGATTCCATTTCTGTGATTCTTGGGTTTCCAAGGGAATTGCCTGT -CTTGTTTCTGTTTTGGTACTGATACTTCCCTTTCTTTTTTGAGGGAAGGTTGAGAGGGGG -GTGAGTGGGTGTAGAATCCTTTTTTTCATAATAAATTAAGGGTTGAAGAAATCACATCAA -TATTTACATTCACATATAGATATCCTCTTTCTAAACAAGAATGGATAATTTAGTAGTCAA -GTCAACTGTCGAACTGAATTGGCAGTGCACAATATCCTCGTTATGTTTACCAATTGATTT -TCAAGAATTCATTGTATTGGTAAGGCAAATGAAGCAGTTGAAGAAATGGTCACACTAAAA -TCCTAAATGGTCCAGGAGATCCGAAGGCAATTCCATGGACTCTCCTCACACCTTTCAAGG -CGGCTGCTGATGGGTGGTGCCATATGGATATCAAAAATGGCGATGTTGTTGCTTGGCCCA -CTAATCTTGGGTGGATGATGGGACCTTGGCTCGTTTATGCTGCATTGTTGAATGGGGCAT -CCATTGCCTTGTATAATGGATCTCCCCTTGGTTCTGGCTTTGCTAAGTTTGTACAGGTTA -ATTTCTTTCATTGTTATTCTTCCTTGGTCTCCTTTTTCGTGTTGAATGACTTGGTAAAAT -CACTCTGTATTACAATTATATACATTTGAGATAATTGTGTCAGCTAATATCTTGTTGCTT -TGTCATCTTCTAATCTGGTGTATTTTCTTGTTGTAAGCTAGGGAAGGTATCTATTTATTT -TAGTCTTTTGAACTTAACTTTTATCTCTTCCTACTTGCATTAGCCTTGCAATTATACTTT -GGGTGGACTATCAGAAAACTAAACAGGCTAAGTTTCTTAATTCCAAAATTTTATTGAAAA -GGAAAAAAATGATGGATGGAAAGAGAACACTCTATTGTATGTACAGTTTTACAATTTTAC -AATTTTATTGCTAAGCCTGTGGTGCTCACCGACCCAACAGAAGTGAACTATTCGAGGCAT -CACAATCTCTGATAGATATGGTATTTTAGAATCTTTTATTCATCGCAAACCTACATTGTT -TAAATGTTGAATACCTTTAGTTATTTATGCTCATGAAAAATCTCCCCTTTGCAAATTAAC -CAGGATGCTAAAGTAACTATGCTTGGGGTGATTCCAAGTATCGTGAGGACTTGGAAAGCA -AAAAATTCTCCTGATGGCTATGATTGGTCAACCATCCGGTAGTTTCTAAGCAACTCTCTC -ATTATGTTTTTATTTCACGAAGAGCTCTATTGGTATCTTCGTTCTTGTTTTACTTATATT -TCTTTATCTCCTTGCCTGTTATTTCCTTCCAAATTGACTGAAATTGCGTGGCAAGCTTGC -ACATGTTTGATTCATGAATTTATATTTCAAATACTGATATTATATGAAAACAATATTTTT -CCTACATATATGCACATCAAAATGAATTCTGCTCAAGACTATTTTTCCTTTCCCTTTCTT -GGGCTTAATGTAGTTCATACATGATCCTAGTTGCTTTGGCTCCACTGGTGAGGCATCTAG -CGTGGATGAATATCTTTGGCTAATGGGAAGAGCTGAATATAAACCGATAATGGAGTATTG -CGGTGGTACAGAGATTGGTGGCTCCTTTGTCTCTGGGTCAATGTTGCAGCCCCAGTCTTT -AGCCGCTTTCAGCACAGCAGTCATGGGATGTAGTCTTCATATTCTTGGCGATGATGGGTT -TCCTATAGTAAGCACGATACAACCTTATATTTGGAACATCAATAGTATTTGCTAGAGCAA -ACTGCATTTAATATCATGTCACACATTTTATGCTTGCCTATTAAGTTCTTCTTAAGCTAG -TGAGAGTTGAGTGTTTACCAAATGTGATCAGGTCTGAGCATTTGATGTAATCGACAATAA -CAAGAAATTTAGAGGATAGAAATTGAATTTAGGCAAAGGAAATTCAACCAAGTAGACAAT -AACTAGATTGAAAGGCCACAAAATCGACCTGCTACACTAAATCCTAGCACCTAAGCTAAG -AACCCATCAAGAAGATAATAGCCAAATCTCTTTGCTTCCTCGCAAAGTTGGAACTGATCC -AATAGATACGCTGACTCCCCTACCAAGTTCATACATCAATATAATCTAACTCTACTAAAT -TGAGAATGTAGGGTATTAATACTACGGCTCAATAGAAGCTAATGAAGTCTAAAATATCTA -CAACTAGTGATTAGAAATACTATGAGACTGAAAAAGGGAAGTTGGAAACATTGAGGTTAT -TCTCGCGATTGCATCTGTCGGGGTGCAATCATGGTCCAGTCTTGGGTCAACTTCCTCTCG -ATAGTGGACTCTAAGGCGCAATTGCGGACCTTGTCAAAGTCAGCACCTTCAGCTTAAGCA -GACATCTTGTCACAATCTCAGATTTCTGTTAGGACTGGTTTATCCACAATAGGGGAACAA -TATCTGCAGACAAGTCATGATCCAAATA diff --git a/probes/mapping/blast/ch12-sc03-4_Product.fasta b/probes/mapping/blast/ch12-sc03-4_Product.fasta deleted file mode 100644 index 6c18e9338104f33e28f37045232fe05757dea763..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/ch12-sc03-4_Product.fasta +++ /dev/null @@ -1,74 +0,0 @@ ->S_lycopersicum_scaffolds.fa_SL2.40sc04057_22823181_22827553_ch12-sc03-4_Product -GTGGCTAACCCAATCGGAAACCGACGCCGCCGATCCCGCCGGCGAGACCAACCCCCCAAC -CATAGACGTATTTGAACTATTTGGTTATTAATGAAGAAACCAAAAATTTCAACGAAGCCA -CATTTACTATGTCACGTAACATACAGTTGTGGCAACCAAAGCTGTTGGGTCGCCATAAAT -TGACATTTCTTGTTTTTTCTTTATAAAGAAATACTCCTCACCTAATAGTATGAGCACATT -GAAAATTTTCAACTACTTTCTCAGTTCTAAGGCCACACCTCTGCACTCTTTATATATTCA -GTATCATTTTTCGTGTCAAAGATATCATAGCTTTATCTCCTCGCAACTTCGCCTCTTATC -CTCCGGTAAGTTGAGGAATTTCGATTATCTCGATATAAGTTATTGTAAATTGGTATGTGT -TCATCCAATATAGAAATGGGGTTCACTTGATTTTGAGATTTGGGGTGGTGTTTGTTTGGG -AAAATGTTAAAGAAATGGAAGCGTATCAATTGTTTGAAGAAATGTTTGTTTGAGTCAGCT -TCACTCGATTATGGATTTTTGACAGCTAGTGCTCGATGAATTAGAAATATGAGAAGATAA -AATGATCTTAAAATTTGAAAAAGGGGCAATTTTGATCTTTGGGGATTTCCGACTTTGTTT -TCCTTGATCATATTAGGTTTAGGATCAGTAGAAATAAATTATAAGTCTTATGAATTTCAT -TGGCTATTTTCAGCTACAAGTAGTATAAGCTATATGGAGCTGGTCAAGGAAGTTGCCAGC -AAGGGACCTGAATCGCAGAAGAATATTGCGATAAGAGCTGATGAAAAGAGCTACAGTTAC -CTGCAGTTGATTTCATCTGCAAGGAGAATTTCAAGTTTGTTAAGCAAGCTAGATCTTAAA -ACCGTGAGTTGGAAATGACGAATTATCTATGAATAACTAAAGCTGCATGAATTTGTGTTT -CTATTGAATAGTGTAAATTAAATGAAAGTTTTCTTTTCCCAGTTGTAATGTTTAGTCGAC -AATTATATTGTTTACGAAATTCATTCAATGTGAGTCCTTCACCCCACATTATCTTTTTCA -TCTGGATATATTGCTCTTCCAATTCCAAGGTCAGTCTACAGAATTTACTTCCGTTATTGC -TTTCTGCTCAGTTGCTTCTACTTTTTCAGGACAAAGGCATCAAAGAAAATGAACATCACA -AAGGAGCAAGAGTAGGGATTGTGTCCAAACCTTCTGCTGAGTTCGTTGCTGGAATACTAG -GAACCTGGCTTAGTGGAGGTTGTGCAGTTCCTCTTGCTCTGAGCTATCCTGAGAGTGAAC -TGCTACATGTGATGAATGACTCGGTCTGTCTCTGAATCTTTGTTCTTCTCCCTCACTGTT -TCATGTCAGTAAAGTGTTTTATTGATAGATAATGAAGACACAAAAAAATGAATGTCTTTT -GCCTTTTGAAATGCTCAATATTAATGACATAGATTGCATTATTTGTCATGCCTTGCTATC -TGTCTGTAGATGATTAGCTCATGTTCAATTAGGCTGAATATTACCTGTCTGCATGATGTA -GAAACACTGCAATGTCCTCTTCACTGTTTTTTTCCTCTTTTATGCTTATTTAATTCATTG -TGAAACATTGATTTCTAGGACATCTCCATAATTTTGAGTACTGAAGACCACCAAGAACTT -ATGAATGCAATTGCAGCAAAAACTGGTGCTCAGTTGTCTCTCATTCCTTCAATTCCTGAT -GTGCATTCATCAACAAAACATGACCAATCAAAAGACATGGTTTCTGACGGTCAACAAGAT -CTGCTAGAGATCAATTCTTATGGTGAGATAATGGGTAATTTGTCTGTTTCTCTATATGGT -TATATATTTTCCCATTTGAGATGTTTGGAGCTCATCAATAGCATTTTCCTTTGTTCTGTA -CATGTTATCTTTAAGGCGAGAACCCTGCTTTTATCTTGTACACCAGCGGCACAACAGGGA -AACCAAAAGGAGTTGTGCACACACACAATGGAGTCTTAGCACAGGTTGATGTCTGTTCTA -GACTTGATATCAGCATTCCCCTGCTTTGTTGGATCTTGATATGATTGATTCTTAGCCTTT -ATGTCTTCTTTTCAAATTCATTGATTTACTAGAAACATTCCACTTCTACTTCGTGATGTT -ACACTATAAATTAAGGCTCAGAAGATATCATTCATATCACAGACCTTGGTGTGTCCAATT -GAGCAAGTTTGCTTCCCCTTTTTTCTTCCTCAATTAGGCTGTGAATGCATATGTATTCCA -TAATTCTGAAGGTAGGATAACATGCGATAGTATTTGTATTGCTGAGAGATGATAAGTAAC -CCAAGTCAGCACCTTGGACTAACTTCTGTTGTAATGAAGAAGAGTCGATATCATTTACTA -AAGTGACCTTGCTTAGATCTTGTTTCAGTTGTCAGTAATATTGAGAGGGGTGAGGATTGT -CTTTATTGAAGTTTCGATATGAAATACTCTTTTCAGTTTACTGGAAGTTTTGTTGATGTC -TGTGCTAACCCTCCTTCCATGTTTGCTGTTTCAGGTCCAAATGTTAGCTAATGCATGGGA -ATACACGCCCAAGGATCAATTTCTGCATTGTCTACCACTCCATCATATCCACATTCCTTT -ATTTTTGTTCCCAATCATGTTGTTTACATAATTCCTGCTTTTGCAATGTGTTTTTGTGTG -GGATAAACAATCTCATTTGGACTACAAAACTGGCTGATCCTTAACCTGTACTGTACATGT -GCATGGACTTTTCAATGCTTTGCTTGCCCCTCTTTATGCAGGTTCCACGGTATAATTTCA -CATCGTCAAACTTTTTTCACTACAGCATACATGCTGTCGGATTGGAAATTCATGTTACTA -TATCCGCTTTTCTCTTTTTGAAGGTCGACTTCGTGCCAAAATTCAGTGTGAGGGGAATTT -GGCAGAGATGGCGTGAATCATATCCTACAGATGGGACTATAACAGATAATGCCATTACGG -TGTTTACTGGAGTAAGTCAGTTTTAAATAGATTAGTGAAACATTTTTGCAATGGTATGTG -ATGTTAGTTGATCTGTGAATTTATTATGTTGAGCTTTGCATTCTTAAACTTACCATGGAA -AAATGATTTCTCGCTTCAGTTACATAATATGTGCATGAAGCTTTGAGTAAGAATACATGT -TTCGTGTTTCTGCATCCCTGAAATGGACTCACAGTGGAAGCCTCTAATAATGTCATCACT -TTCTTAATTTATCATGAAACTCCATTGCATCCTGTTTGCATCAAAGCTAAGAATAAGAAT -ACATGGTTTCTCGATTCTTTTGCATAATGCTTTCTTTATGGCTGAGACTAATAATACCAT -GTCATGATCTGTGATTTCTGTATCCTTGGATAGGAGATACTTACAGCAGAAGCTTCTACT -TAATGTCAGATATCTAAGATGTCACTACTCTGATTGTATTTGGGGTATCGATACGGATAA -CTTTAGCTATTGTGTGTACCTAGCTTGGATTTTCCAACGCTATGTGTCAACTAATAAGTT -TGGTAGCGGATCCACCGACTCCTACCCTCCACTCTTTTCTGATTGATTTTTTTTCTAATC -CAATAGGTTCCAACTATGTATGCACGATTGATACAAGGTTATGAAGCAATGGATCCAGAA -CTAAAAACAGCTTCTGCTTCAGCAGCAAGGCACTTGCGCCTTATGGTAATAGACTTGGTT -TCTATTTTGCTGGTGTTTTTGATAAACAACATAAAACATAGTTAGGATCTTAACTGTACA -GAGCCTGCTTCCTCATTTTGTTTTGTTTTGATTGAGTATAGAGTGTACTGTTGTCAAAAC -CTAATGTGTTTTTTAATCATCCCAAATGAGAAAAAACAATGATTTCTGCTTCCAGATGAG -TGGCTCCTCTGCACTTCCTCTGCCCGTCATGCAGCAGTGGGAAACCATTACTGGACACCG -GTTATTGGAACGTTATGGCATGACTGAGGTAAATGTGCTCATAGCCACTTTTAGTATGTA -GGATTTTGACTGTTCATTTAATATCTATACTTATGTAAATGGTTAATTTCGTCTAGTTTG -TGATGGCAATCTCTAATCCCATAAACGGCAAGCGCAAAGGAGGTACTGTTGGCAAGCCAT -TTCCAGGTGTGCAGGTTAGTGAGTTCCTTATGTTATGTTCTCAACATCTAATATGCTGCT -GCAACAAAGTCCATAAATGCAGCCCAAAATTTTTGTTAGATATATCCCGTATTTATGATA -AGGTCTATCTATTTTTCCTGAATAGTCTATCACTTCTTTATTTTGTTTCTGATAGGCCAA -GATTCTTTTGGACGATGCGAGTAGCAATGACCAAACTGGAGTTGGGGAGCTCT diff --git a/probes/mapping/blast/ch12-sc03-5_Product.fasta b/probes/mapping/blast/ch12-sc03-5_Product.fasta deleted file mode 100644 index ba22bcb6c0b00f579f1720ed2d683bcdc4be0470..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/ch12-sc03-5_Product.fasta +++ /dev/null @@ -1,71 +0,0 @@ ->S_lycopersicum_scaffolds.fa_SL2.40sc04057_23797776_23801944_ch12-sc03-5_Product -AGAGTCCGACAAGCCCTGAATGAAAGCAAGAAAAAAAACTATAAAGAGCTTGGAGTAATG -TCGAAATACCTCCACAGAAAGATGTTAATATCAACTGGTGCAAATGACAGAAATGACTAC -CTGTAGAGACATAACCCTTTGGGATCGAAACTAGGAGAAAAGAGGCGGTGAATAAAGTGA -TGTTTTGAAGTGCTTCGGTTCTCAAAACTAACCACTCCAGAGCACCATTTGAGCAAAGAA -AGACTTTTGCATCTGCATCGACAAGTTTTAGGTAATTTTGAAAGAATCTGTCTACTGCTC -CAAATGACCTTATTGTGGCAACTCCAAGTGATGTCTCAGTTACATAATTCATAACAGGAG -CCTTTGTTGTCCCATTGATTCTCATCAGCTCCTGGGCAGAGGGTTGATAATGTCCCTTCA -GATACAGAAAAAAAATATTAGTACAAACTAACAAATTATATTAGCTTTACGATCAAAAGT -ATTTAGCGGAAATGAAACTTTACCTGGACATATTTTGAGCCCACTGTAGCGATGATGCCC -ACAAGGAGAACCTGCCATGTCACTGAGGCCATAATGCCAATTGTTACAAGCAACTCCATT -CCAGCAGCCATCACAAATGCATAGGAGAATGGGATGTCGTAATCTAATACACTCAAATCT -GATGAAGCCTGATGATCCAGATTAGTAGGCAACAATCAGTGAAACTTGTTCATGTCACAG -TGTTTTCCGTAGTCATAGGTGCAAAAGAAAAAAATGTTACCCGGGTTAATATCCGTCCAA -CTGGGGTAGAGTCGAAGAACAACATAGGAGCATTGAAAATTGAATTTGTGAAACCAGAAA -AGAAGGCTTTAGATGCTTTTAATCCCAGGAGAGCTGCAAAAAGAGATCTGAGGTACACGA -AAAATGCACTAACTAATGACACTGAACTATAGACACCAATAACCATGATATGACTAATTT -TAGGACTTTGAATTGCAACTGCTAGCCAGTAACTTGCAGCAGCCTGAAGACCAACAAATC -CCGCCTGAGTAAGTATGTTGGAACAAAGGAAGAGCGTTCCTTTAGAGATTACGACATAGT -CTAGGAAGATCTTCCATATTGCACTTTCACTTTCTTTTTCTTCCTCATGTGTCAATTGTA -TTCCGGGCTTTAATGTAACTTCTTTTTGGCTGTTTTCTTTTATAATATCAGTCTCTTCTA -GCTCATGCGATTCATCTTTATAGGTACGAGGATCAAGTCCAGCTACAGCATCTCTGTGAG -CATTCACAAGCTGTTCAAAGGCCATCCCAGACATCAATAGCTCATTATAACTTCCTGATT -GAGTAATTTGTCCACCTTCCATTACCTGGTAAAACAATTAGCAGATAGCTATAAATAATT -GACGTGCGCTAAATGAATACAAGCTGGAAAAAGATTCTAACTAGTCCACATTAGTTACCA -GAATTTGGTCAACCTCGGAGAGGAACTCCACTTGATGAGTAACAAGAATAACTGTTTTAT -TCTTTAGAGCAGTCATAACACAATCCTGCAATTATGTGGAAACAACAAAATGTTGTTGTT -TCTTTGGTCAGTAAATGTTATCATGCATGATAGCAAGTTTTTCACAGTTAACCTCACATT -AAAAAGAGTTGCTGCTGTGTGTGCATCTACGGCGCTAAAAGGATCATCAAGAACATAGAT -ATCAGCATCACTATATACAGCTCGAGCAAGTTGAATCCTCTGCTTCTGTCCTCCACTCAT -ATTAAGACCTCGCTGACCTATCTCCGTGAGGTCACCATAGTCAAAATTATCAATATCTTT -GTCTAGAGCAGATACCTTTACCGCTTCATGATATTTGTTTTCATCCATTGACTTCCCAAA -CAGTATGTTATCACGGACTGTTCCACTCTGGATCCAAGCGGTCTGAGAGACATAAGCGAT -GGATCCATATACATGTACCTAGAAACAATTGCAAGGAGAGTTGAAATCAATTATAGGAGA -TACTTAAGAAGTTCATGATATGAGGATCGCGTTACGACTCACTGTTCCTGCAGTTTTTGG -TATTTCTCCAAGTATGGCATATAGAAAGGATGATTTCCCAGCACCAACTGGTCCACAAAC -TGCAATCTTCTGTCCTCTTCTTGCTTGAAAATTTAAATTTTTAAGCAATGCATCAGGTGA -CTGTGGATCCCAGGTGAAATGACCACCTACTATACAAACACTATGATCTGAATCCTCTCG -AGGAGATGTCACTGCATCCTCCGGTTTGATTTCATCTTCAAGTAGGAAACTATTTATCCG -ATCGAAAGAAACTTTGACTTGAATCACAGCTGACAGCGCTTCTGGTAGATATCTAACAGG -TTCCGACATGGTCCTTAAAGCTGCCAACACAGTGAAAATTGTAGCAGCATTAAACGGCGC -ACTCCTGAAAAACACAAGTCCTAAGAAGATGACACATGAGACTATTGTTGGGGACATCCA -ATACAGCAAAGTGCTATAAGCTTTCATAATCTGAGTTTCAGCCAACCATTTGAATTCATC -CTCCCTATGTGAGTCAATTGAGTTCTTGAAGTGTTCTTCCCATGACTGTAACTTGATTAT -CTTCATACTATTGAGAATCTCAGACATGAACCTGAGACGTTTATCTTGGGCAATCATAAA -TTCAGTCTGACATTTCTGAAGTATCTTGGCAAATGGAACATTCAGCAACCCACAGATAAT -GAGGGGTACTAAACCTGGAATTGCCCCGAGTCCTACAACTCCGAAAAGTACACCAACGGC -TAAAAATATTTGTAGGCCAGAGCTCCATCCTGTGTGAAACCACATCAGAGCTTCTCCCAT -CCGGTAAGCATCCACAGAAATGTAGTTCACTATCTCTCCAGTTGAGTGCCTACACCTGCC -TAAACTCGAGAGCTTGAGTTGTTTCTGATAAACTGCCACCATTAGAGCCGATCTTATTCT -CATACCAACCCTTCTCGAGTAGAAAAAGAAATGTCGAGAAGAAAGAGAATCAACAAGCTT -GTCAACAACCAAGCACCCCAATAAGAGAACACCTTCAACAAAGGTTCTTGTCTCGCTACT -TGAATAAGCCACGAATGCATATAGCATTAAAGGAGAAACTACAACAGCAATAATCCTGAG -AAATACTAATGCTCCTGCAAGAACCATTTCTTTCCAGTAAACTCTTGCTATGGCCTTAAT -GAGAAAGTCCTCTGAATTGTCCTCTCCTTGGAGAGATTTCCATTCACGAGACAATTGCTC -GTAAGCTAAGATGGCTTCATCTTCATATCCTAGACAAGGAATATCTTCAAGAGCTAAAGT -TTTTGAGTTTCCTAGACCAAGCAAACCATTAACCCAAGAAAATGACAATTTGCCAAAAAG -ACTAGTATTTCCTATACTAATTAGTTTGTCATCAGGTCGATCAACGAGTAGAGGTTCCAA -CAAACTCTGCTTTGATGAAGATTGAGAAATGATTTGATGAAAGGTAAGTAAGGCATAAAA -GAAAATCAAGAAAGTGACTAGCCATGTCACCAGGTCTAGTATTGGGACGCTGCGAGTTTT -CATGGATACTTCAATAGTAAGAGTGGAACTCAACAGAAAGAAAATCACCCACCAAGAAGA -TATCAGTATTTGAATCCATTTAGATCCTTGAACAAGCAACGATACAGTTAAACTGATCCA -AATCATTCCGCAAACAAAGCAATGTAACCAACTAAGATGACTAACACCACCATCTTTACT -ACTAATAAATTTCCATAAACCAAGACCAAAATACACAATGCTTACAAGAGCACAACAAAC -AGAAACTCCTATAGCCATCCAGTTCCTCCTGCAACCACCACTAGTAAGTCTGAATTTTCT -CACAAGACCGACAACAAGGAAAAGAAAAACTAACAAGAGATTCAAGGCATCTACTATTCC -TCTATGGATGCATAGTGAACTCCAACTGAATTCTCCTCCACATATCCACAAGAACTTTCC -TGCAGTATTCAAATATATCATGAATCTCAGACTCAAAATTAGTCAAGAAAATATAAAGAA -TGTATTGATACAAAAAGGAACTTGATCGAAAACATTTAATTTGAAATCATTGAACTTTTG -AATAAATCAAATATACTTAGTCCATTCAAATGAAAAGCTAAGAAGTGTATACCAAGTTGA -GGAGCCTGTGCAGAAGCCATTGTTAGATA diff --git a/probes/mapping/blast/ch12-sc09-1_Product.fasta b/probes/mapping/blast/ch12-sc09-1_Product.fasta deleted file mode 100644 index 3f02ff2767ad4c3c91b03dd45c21eb1852856303..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/ch12-sc09-1_Product.fasta +++ /dev/null @@ -1,32 +0,0 @@ ->S_lycopersicum_scaffolds.fa_SL2.40sc05611_353222_355021_ch12-sc09-1_Product -GAGTTGGACAGTGATTGGTGGGCAACGGGTTGTTTTTTGTTTATGCTTGTTCTCGTCACA -CATTACCCGTAGACTGACTTCATAGTTAAGGTTAAAGTCTAATGCTTCTGGCCAAGTGAG -AATCTTTCTGCTTCATGGACTTTCTTTAGCTGGTTTTCAGGATAGTGTTCCTGGCTTCAT -AAACTGATTCGTTTTCTCATAGTGAATGCTTATACCAGCTTTAAGAGGAGAGGCTTAACC -TAATACATGTTTTGAATCTTTTTTATCATACCTTTTTGTAGTGCAGCATTGATCTTATGT -CATCCGTCTAGGGTAACTTGTTCTTGTTCTACTTTTATCATGAAGTTATTGATTCTGTTA -GAATATTAATAATGAATGCGAATGTGGAAACTGATATATTAAAATGTTGCTTTCTCTGTG -AAAGCTTCCTTTCAGTTTAGTCTAAAGGAGTACATATAGAATATCCCCGTCTCTTATCCT -ATGGACTTAATTTTTTATGGACAGGATTATAGGCAAACACATCCACATGTCGCGGTCCTT -GATCCTCCAGATGCCATACAGCAGGTATATAATCGTCAATACATGCTTGAAGAGGTTGCA -GACTTGAACTTGTCAGATAGCTATGGTAATTTTTCCACTTCTGTTTAATGATCAACAAGA -CTTTCGTCATGAACTTATGATTATCTATATACAATTGCTGTTATCCTGAAAATAGGGAGT -CTGTTTATTAGTTGTATGCACCAAGATTGTCAATTTACAGTTCCTGGAAGGCTTTTGATA -AAACTGTTATGCTTAAGTGATGAGTAACTTGCTTTTGACAGGCAAAGTAGGTGTTCCCAG -GCAATTGGTTATAGAGAAAGATCCTTCGTCTATCTCAGATGCAGTGGATAAAGCTGGTCT -TTCACTACCTCTTGGTAAGTATATCTATATTTTGTTGTTGCTTATTTGGGATTAATCAAC -TGATCGGTAACCATTTTTTGAACTTCCACAACTCGATAAAAGGTAGGGGCTAGCTATCAG -ATCTTTACTTGCCATGGATGCAAGTCTGAATGAACTGGTAGGGCAATAGAGGGATAGACA -TTGTTTTTTGCGGCTGTTCTTTTTTCTGAATGGAGTTGTTTTTGTGTTCTCAGTGGCAAA -GCCTTTGGTTGCAAAGTCACATGAGTTGTCTTTGGCCTACGATATGGTCTCTCTTCAGAA -GCTTGAACCACCGCTTGTTCTGCAGGAGTTTATCAATCATGGTATGTATTTCATTTAAAG -GTTGAATTTGTGTATTTCATGTGCAGTTTTGCTTGAATTAGTGAGGTGGTGATACTTTGT -CATTTTTGTGGTTGTAGGAGGTGTACTTTTTAAGGTTTTTATTGTTGGGGAAGCCGTTAA -GGTTGTCAGGCGTTTCAGCTTACCAGATGTTAGCAAACTCGAGCTGTCCAACAATGCTGG -GGTTTTCCATTTCCCTAGGGTTTCGTGTGTTGCAGCATCTGCAGAAGAAGCTGATTTAGA -TCCTAGTGTTGGTGGTAAGCCATCTTTTTCTATATGAATTTGGTTACATTGTTGTACATA -CCAGAATGTATCTAGCGCACTTTAATATGTAGACACCTATAGATATGGCTTTACACTTTG -TTGGATAAATCATACAAGTTTCTTAAACACTTGATTCCTTATTTTCAAACAAGTGGGAAG -ACTTCAAAGATTCTTGTCCATTTGATAAAATTATCATTTCATTTTTCCGGCTATAGATCG -CCAAGACTAGGCAAGGATGTGATTGATTAAGGGTATCGATACTGTTCATAAAGTCCATAG - diff --git a/probes/mapping/blast/ch12-sc09-2_Product.fasta b/probes/mapping/blast/ch12-sc09-2_Product.fasta deleted file mode 100644 index ba28b5ccbf280f3b798b000018ffa419115b16b7..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/ch12-sc09-2_Product.fasta +++ /dev/null @@ -1,35 +0,0 @@ ->S_lycopersicum_scaffolds.fa_SL2.40sc05611_528593_530597_ch12-sc09-2_Product -TTTGCTGAGCTGGACAACAGAGCTACTATGCTTTGAACTAACCGCGAATTAATCTTACAT -GAGTTACATAATAAGCGGAAAAGGAATCCATCCTTGTTATAGAAAATATTAAATGTTATT -CTGTTTGCTTATGAAATATGAGAACCTTCATTTTCTAAGTGATTCTTGGATGATTACTCC -AGCTTCCTGTGTTTTACATATGTTTCTTTATAAATGATAGTACAGCCCACAAAGATTTGA -AAACAATGTTATGTTTTAAGTGTTCATAGACAATTGCAACATCATTTTTTTTGCATTTAT -TGTTCTGTCTGATAGAGAAAGTGCAGGGAGAATTGTGATTACAAATGAGTAAGAAGGTTG -TCGATATTTTGGCGTGGCCTACATTTTGCTAGCAATGGTATTGCCTTGGGCATAGTGAGT -CCAGGTCCTCCAGTCATGTCAACCAGCTCTTCACTTACTCTCTCCCATTCAAAGCACTGA -ATAAGTGATCCTAAAGCCAAACCAGCCACATGCATTGCCATATTCTCACCTGGACATCCT -CTCCTGCCATATCCAAATGGCATTAGCCTGAACCCATCTCGTTGACCTTTGAAATCGATA -AACCTTTCAGGCATGAACTCATTTGGCCTGTCCCACAACTTAACATCATTTTGTATTGCC -CACAAATTCACTAGCAACATTGTCCCTCGGGGTACACGAAAACCTCCAACAACACACTCA -TCTGAGGACTCGTGCGGCACAAGTAATGGAGCAGCTGGGCACAATCGGAGAGTTTCGTTT -ATGATTCCATGGAGATAAGGGAGTTGAGCAAGGTCTGACTCATCAAGTAACCTTGATGAC -TCTCCAAGGTGAGTGTCTATTTCGTTTTGAGCTTTCTTTAGTGCCTCAGGATTGTTCAGA -AGAAGTGATAATGCCCATTCCATTGTGCTAGCTGTAGTATCAGTCCCTGCTGTTAACATG -ACTATTCCCATGCCCTTTACCACTTCATCTGTGTAATAATCAGGCTCTGAATCTTGGAGG -GATAACAGAACATCAATCATGGTATTGTTCTTTTGCTCCAAATAAGATCCCTTTCGTCGG -TTCTTGTGCTCTTCAATCAATTCTTGCATGAATTTATCCCTCTTCTCCTGCAGTAACTTC -ACCTTATCCTCAAGTTTGTTAACTCCTATCCATTTAAGAAGTGGCACAAAATCTCCTATA -TTTGTTGCACCACTCACTTGGAAAGATTCGATAACAATCTCTTTAAACCTCCTAGATTCC -TCCAATTTCCCAGCAGAATCACCATAGTATCTTTTCCCAGCGATCATCATCATCATGATA -TTCAGTGTCATCTCAAAGAAAACCGCTTTCATATCCACCACGTTTGTGTTAGTATCTCCA -CCACTAGTTTTCCCCCTTAGAAGTCGTTGCAGCAGAGCCCGAACCTCATCTCTATGGATA -TCAGCGAACATTTGAACTCTCTGAGTAGACAAAACTTCATGAGTAGCAATCCTTCTTAGG -TTGCGCCAATGTTGGCCATAGGATGCCCAAACAAGGGTGGTGTAGTTGTAACCAATATGT -TTTCCAGCAAGCAGATTCACACGATTGGCAAAAACAACGTCGTTTTTGGTGAAACATTCC -TCTGCAAGAGAAGGGGAGGAGACAACCAGGACAGGACGCGATCCAAATCGAAGGTATAGC -AAAGGACCATGTTTTTCTGTTATGTTGGCTAATGTTTTATGAAGTGGTTTTTTGTTGAGT -AGATATAGATGGCCTATAATGGGCAAAGAGATAAAGGGACTTGGTGGGAGATTTTGGAAT -TTTCTAAGGAAATGGTTCTTTAGAATGTAAATGAAAGTGAAGATGAGTGTGTAATATGAA -ATTTCCATGGTTGATGCAAATACAAGCAAACAAGACTTTTTGATAACTTTGCTCACTTGA -TGATCATTATTTATACTAAAATGTTGTAATAAGGTATCTTTTGTGGATGGCAAAGTGCCA -AGCATGCTTGTATTGTCAAACTAGG diff --git a/probes/mapping/blast/ch12-sc09-4_Product.fasta b/probes/mapping/blast/ch12-sc09-4_Product.fasta deleted file mode 100644 index 63aa3208b115437f09941e068685dd868b0c67aa..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/ch12-sc09-4_Product.fasta +++ /dev/null @@ -1,61 +0,0 @@ ->S_lycopersicum_scaffolds.fa_SL2.40sc05611_967164_970727_ch12-sc09-4_Product -GACGCTCGCCTTCTTCATTACCATGCCAATCTTTTTCTACAACAAATTGTGGTTTCCATG -CGATAAGAATACAATAACAGCGATAAAAAAGTGCATTGTTGATGCGGCTGATTTAGTAAA -TTTGAAAACTATAGAAAGAACTGAGTTACCTGAATGAAATCTAGACGATTTGATGTACTG -TCCATCTCCGTGTCCAACTCACTTAAGATCTTCTCCTGCAAGAACATATATTGATTTTAA -CTACATTTTGCTTCGGAGGAGTTTAAGCAGAGCTGCAATTTGTTCAGTGACAAATTCAAG -GAACTGGTTAAGCAGGTGGTCGCACTCACGTGTGCAAGAAGTTCATCGTGTATGGTGAGC -CCAACATCTCCAATTCTGACTACGCTGGCACTAAGCTCGTCTAGTTCTTCATCCTGTTGC -CTGCACAGACGATCAAGAAAATACGCTTTCTGAAAGTTATACTTAAAAGCTATAAAAATG -ACATAGTACCATATCAAATAGATTCAAGATTATGCTACATCCTCTAAATTCTACGTTAAT -TGAAGTCTTCTCGACATAATTTAAGTGCTGGCAAAACTATACTGCTAATACCTTTAATAA -CAGGTACTAAAGGGTATTCAATACAGCATACTATTCCATGATAAATGAAGTTAAGTAGAC -AAACTCAGAAAGCTAAAAAGACATGGCAGAATGGTTATGACTATGACATAAAGATCTTAG -AGAGGCTGATGATACATATTATCCTCCCCTTATAAATAAAATCAAAGGCTAGGATTCCAT -AGTAAAGATTGAGAAAACATTAAGATGCCTCAGAAAGATAAATGGATAGGTGCATGCAAG -ATTTACAGTGAGATCGGAATAAAAATCAATTGGTAATAAAAATGACAAACAAGGATAGAT -GCAAAGAAATGGAGGGAATATTACCTCATAAGAAGTAATTGTCTATCTGATTCTGATGAT -ATGAAGTCATCATTATCTCGGGCATTGTATGCATTGGATCTCTCTTTCTGTTCAGAATCT -GGCAATCTCAACAGTTCTCGCCGCATCCCACTCAGATTAGATGTACTTGTCCCATTTGAC -TGTTTTCCAGCTACTACAGCTTTCTTCATGCTTCCCACCTGGTTAAAGGCAATTTGAAAT -CGTTTATTTATTTTCAGGAACCAAGAAACAAAAGAATAGATATTTGGCATCAACAGAATC -AGTTATACTTGAGCACGGGCATTGCTGGTCCATCTTCTTCTCTTATCAAGCTCAATATCA -TTAATACCATACCAAGAAGGATCTCTTGCTGCAACATCAATTGTTTTGTCCAATTCATCC -ACCTTCTCATCAAGAAAACAGGAATTCAGCATTGATAAGGATATGAAGCAAGTCATAGCA -GCAGTAGATCAATATCAAATCACACTGACAGAAGAACAACTCTGGTTATGTTGCTATTGT -TCACTGAAAGAAGAACATCTTTCCCTAAGTACTAAAGTCGACAGATTGGACAGCACAAAT -TCATAGACTGAACTTAAGACAGGTGCAACACATCAAACATGCAATTGTCTCTGGCTATTC -AAAATTGTCGTAATTCATTCACGTAAAGTACAGGCAATCAGGAAGAAATATAATGAGAAT -TTAACAGACCAAACAGTGATAAGTATCAATTAACCAAGTTTCAAGGAGCTACGTTTCCGC -ACATACCTGCCACTCAATGCTCTCAGATGAAGCAAGAAGTTCTTTGGTAAGATGTACTTG -CTCACTACTTCCGGCAGAAGTTTGCTCCCATTGATGAAACGTGGACAAGAGCTTGTCAAT -CTAACCAAGCAGGAATTTCAAGAGTTAGATTAAGTAGTCAACAAACTTGATCACATATGA -GATCCAACAGATTCTACCAGCAAGGAGAGTCTTAGCTTATTTTTTCTTAATAGTAAAAGA -GATGAAATTTCTTAGTTTGTTCAGCTTGTTTTTTTATTTTTTCTATGAAAATAGACAATA -GCCACAAGAAAATCATAGCTTTCTTACCTGTTAGCTGTTACTGGAGTACTTGATTTTTAA -ACCTTAGTCTCGAAGAATTATACTTTATCTCATAGAAACATTACTCACCCCCTTCCCAGA -ATGTCGAGAGAGATGGAGATAGATACATGACAGGAAACACCACCAACCCTTCATGAATCT -ATCTCCCATGCAAGAATAAGAACAACACACTAATAAAAAAAAACAAATCTCAGACGAATA -AGATTTACTTCACTTCAAGATTATTAGAACATAACTAGATCGAAGTAGATGAACTTACAG -ATTCTTGAATTTCCTCCTTGACAATATAGAAAGGATCTTGAGCTGAAGACATCTTCAACA -CCAACTGTAGAACATTTAAGTGGACACATCAGATAATTAAATAACATATATAATACATAT -AAAAAGCATCAGGAGAAAGATGATCGAGAACTATATCTTATACCCAGACATTGCAAAGTA -GTACATCTCAAAATGCCTTTTCCGTAAAGTGTATTATGACAGAGAGATACAGTGGCACTT -TAGCAAGAAGGGCTTTTCCGAGAAAATATGAAAATTACCAGAAGGATGAATTCCAAGAAA -AATAATACTCCTATACATGACCAAATGATAATTATCTCCAGTAGGAAGGCATTACAAATA -TCAAGTGCAAAAACTCAAAATTGTCCCCGGACTCCCGTCAGAAAAGAGTTAGGAGTATTT -TGCTTGTTGATATATAACGCTAAGCATAAATGTGCCTTTATGTTTGTTCAAAGTGAACAC -TTTTGGTCTGGGCTGAACCTAAAATACTTAAAAGCTAATGGAGAAGTGCAAATGCTAACA -GTCCTATAGTAAATAAGGTGAACAACCTGTCTTCTACAACTAACTCGTCTGAGAAATGAG -AAAAAACGCAAAGAAACCCAACTGAATCAAACCTTAACAAGTCCATGTTACCCTTCAGGT -TTGTAATGGTAGTTGTTATTGCTACAAGAGTTCCAGATTGCCATTCTAAACCTTTCGAAT -ATGAATTGTTGGTTTTTCAGGTAAAGCAAAGAACTCAAAGTTCTCTTTTTAGATAAGAAA -CATTTATCCATGAGATGAGAACAAAATATAACTCTTAACAAAGGAAAAGGGTCCTGTGGA -AATCCCCATACAAAATGAGATTTGTCAAAATTTTGGAAAGTAAGCTTTTCGTAGATAAAT -TCCATCCCAATCCAATTGAACTCACAAAATTCAAACTAAACTGATCCTCTTTTGATAAAT -GGAAAGACATAGGTTTGTGTCTTTCATTTCACGAAACAAGAAAAAAAATGTGAATGACAG -TGAGGAACATGGCACATGATTTCATGGGAATAGACCAGGGTGAGAGTAGCTTGAAATAGA -CCACAAACCTGTGCTGATATCCATTAAAAGGCCGATGTGCAGTATATATTTGGGCATTTA -TATAGCCAAATCGGCAATCTAATGAGCTCCTTGATGCATTCAACTCAACATTAGTTTATT -GCTTTTTTAGAAATTCAAATCATTTGTACATGGTTCGTATCCAAGAAAGCATGATTCACA -AAACTTTTAATTGACATTACTGAA diff --git a/probes/mapping/blast/ch12-sc10-1_Product.fasta b/probes/mapping/blast/ch12-sc10-1_Product.fasta deleted file mode 100644 index c789afad706b863997fd1c5873c687c3a4215e18..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/ch12-sc10-1_Product.fasta +++ /dev/null @@ -1,53 +0,0 @@ ->S_lycopersicum_scaffolds.fa_SL2.40sc05380_1864775_1867879_ch12-sc10-1_Product -AACCACCTCCGGTCTACCATCTCTAGACTACACTCATGGGATTGCTATGTTGTATATTCC -TCGTCCATTGTTGAGGTTCGTTTATCAACAACATACGTGGATCATCTTCTCCCTACCTCG -GATTGTAGAGAGGTTGTTTCTAAGGTCTGAAGGAAAGACAGTTCAAAGTAGTGCAGCAAA -AGAAGTGACAGAAGTACAAAGATATAACAACGAAGAATGATCATAGAATGGAACTTCATG -GACATGTAGTAGTTTTCATATTCATAAGAGGAAAAAAGTATCAAAATACAAAAATAATAT -ATGAACCAAGTTTGCTGCCCTCAACGACTGAAGTGACAAAATTTGCAGCATCCTCATCCT -GCAAAGCAAGCTTTGGTTTTACTGACATGGATCTTATTGAGAAGAAAAACTTGGATTCTA -TAACAATACCAATACACCATGTAATCATCATCAGTGTAAACTAAACATGTAAATGCTTAA -CGCCTCAACTTAGATTTGAAGAGGGAAATTTACAGCATATCTATCTAGTAAAAGAGGAAA -TTACTAACCATCTACATCGAAGTGGCTCATGCAGAACTCATTATTCCTCCCTCTGAGGAT -TGAAATTATGAGAGGAGAAGACGTAAAGACAATAACAACAACAGAGAAGTATATTGAACG -ATAACTTGTTCAGTACACAACAAATTAAAGATGTTTTTTTTCTCCCTGAATTGAATAAAA -CAAAAACAAAACCGAGTGTTGTGATTCTGCAATAAGAAAAATATGCAGCAGGGGTAAATG -CAAGAAGACAGACAGTCTGTTATTGATCTAATATGAAATGCGAGCTCTATTTGCAAGCAT -TTTGTTTCACATATAAAGACATTCTACTATCAAAACAGAGTCAATGGCATCTTATCTGCA -AAACTGATGAGTTCTTATCCAAATGACCAAAAACGAAGATACAGGTGTAATATGAATCTT -TCTGAAGCAAAATCAGCAGGAAATAAAGTTTCAGTTGAAATCCCGCAATCTCTTCTTCAA -GATATCCATTGATTTTTTACGAGCACTCTGCTTTGTGTTTCTGCTCGAAAGACTTCCAAA -GAGTCCATCCGCCGAATCTTTATACTTGTCACAGATAGTAGAAACTTTTTTATGATCTAG -AGCATTATAGTTCTTCTCCCTTATGACAGGATTCATGAAGTTCTCTGGTTGACTGCTTAG -GAGGAGGTTTATTAATTGTCTAACTTCTACCAAGCAACTTCGAAAGCTATCGTCCTTGTA -AACCTCACTCAGCCCAGTACTATCAAACCTCTCATCAGCAAAAGACTCCAACGCTTTCAA -ATCGTGGTTGATGCTCATTACTGCATTAACATTGAATCTCTTTATTGAGTCACTCAGAAA -AGTTGACACAATTGAATTGGAGATATGCTCCAGAGCTCCAATCCCAACTTTATACAAAGC -ATCCAGAGGTAAAATTTGTTGAGCAGTAGACAAGAGGGTGTCGAGATATATAACCACCTC -GTTCATGCATTCGTTCCCTTGCTGTGGGGCATCCTCTGCTGTCCAATGGACATTTTCTGT -GAGTGACATGAACTCATCCAGTTTTGCATTAACTAAGCTTAGTAATGCAATATAAGCAGC -ATCTCTTGAAGTCTTGAGGACAATCTTGGCGGTTAAACTGCCTTGAGGCCTTTCAACTAA -ACGGACAGGAATGCCACATTGTTGGGCTGCATGTTGAAGAAAGAAATCACAAGCCCTTTC -AAAAACAGCTATATTTGCAGCAATTTGCATTGCCTGAGACACACCAGTTGTACCACTGTA -GATAGTCTCAAGTAGGACTTCATTCAGTACATCAATCAAGAGCTTATCCAAATACTTCTT -GACAAAATCAAAAAAATTCATTTGGCTCCCATAGGATAAGTAATTGACAGAATCTTTGAT -GAATGACTTAACGATGCGACAGCATTCCGGAACCATGGAAGAGAATGGAGAAATAAAAGG -GAAAGCTGGCATTATATCAGAGGTTTGTAGATGGAACAATAAAACATTTGCCTGATAATC -TGACTCCCTCTTCATAACCATCTGCTCAAATGTATCATTGGTGACTATAGCAGTTATTTG -TTGCCTACACTCTGCCAAAAGAAGTTCATGGTATTTTTCTCGACTACTATTTAGAGTCCC -AAGAATCGCGCTCACTTCATAGCCATATTGTCTGAGGGTTGACCCAAGAAGAGTCACATA -ATCCTTGACCATGAGAAGATGACTGGCACTATCCATGTGGGAGAACTGTTCTTCCAAGAG -GGCAGTCACTTTACCTACAGCTGTTTCCCACATTGTCTCAACCTGATTAGGCAAGAGCAG -ACCACCAGCAGTCCTTAATACTCGATCCTCAACAATAAAATAACCTGCAATCTGTGCCAA -GAAGATTTGATGGGATTCTATGAATGGTTGTGACAATGAAATCTGCAAATCTGAACTCAG -CTGCAATAAGCGATTCTTATAGTAATATTCACGAAACTGCTCTTGGATCCCCATACAACC -ATGAATGTGACATGCTCGATAAAGAGGCGTCAGGTCAAACTTTAAGACAGATTCTTCATT -AATCTCCTCAACATCTAGGGTATAAGTGAAGTCTCCTAACCCCAAACAACTTTGTTCCTC -GGCTTTTCTTTGACGGGCTAGCATATCCTCATCCCTTTGACGAGCAGATGCAGCATATCC -TATTGCAGTTTGCCCAATATCCTTTGCTGTACTCCTTATGTGAACTAGCCATTCATTAAT -TTCACTGGTTACTCTCTTCTCAATATGCAATTTAATCAGTGGTATTCTCTTCTCTATCAT -AGTCCTGAGTGGCTTGACGGGAATGTTCTGCAAATAACTTTTTTCAATCAGATCAATAGC -CTTGATAGCAGGGTAAAACCGACCTTCAGAAACGTGGTTGTTACACTTTGCACAAAGTTC -TAAAACTTGGACACAGTTGCCTGACATCTTAATTGCTTCTGTAACATTTTTCTTAATTGA -AAAAGTTTCAAGAAGTTCTTCAAGTTTTAAGAGAAGGACACTCCCGACATCTTGCAGCTT -CAGATTATCAGTTTGCAACTCAGCCTTTAACTCTTCTGCATCAAC diff --git a/probes/mapping/blast/ch12-sc10-2_Product.fasta b/probes/mapping/blast/ch12-sc10-2_Product.fasta deleted file mode 100644 index 3ff4a93afc4b65100ab52109dfefb98fc04580eb..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/ch12-sc10-2_Product.fasta +++ /dev/null @@ -1,61 +0,0 @@ ->S_lycopersicum_scaffolds.fa_SL2.40sc05380_1423814_1427393_ch12-sc10-2_Product -ATTTTGAGATGGGCTGCTCCGATCTGACTTTAATATAGCTTTTCTCGTGGGTAATTTCTA -TAATCAAGGGCTGAATGATCCTACTGCAGGCCACTACACTACATTTTAAGCAACATTTTA -GTCAGTGTTGTCGAACATTCATTTAAGGTCCACGCCCTGAAGCTCAGAAAATCTCAGGCA -GGCGCTTCACCTCGCTGAAGTTGCGCTGTGAAGGCAAGAAAATGAGGCTTGCACACCACT -GCCATGAATTCTAGCTTGAATGGAGCTGTATTAAACAACAAATTTAATCGGCATATAAGT -GTATTACATAGTTGTCAAGGAAAAGATTATGAATGAAGTTTGTTACCTTTTACTTGAATT -ACATATTTATGTATAAATATGTTTTTCCCCTCCCATTGCACCTTATTTTTACCAAGCCCA -CACTTCAATTTCACATTGCACTTAAAGATGCAATAGAACTAACACGCTTTTTAGAGCCTT -TTACCTTTGGTGCAAGTTTCAACTACATATTTAATCACACAGCGAAATCAGTTGATGTTG -CTTGAGAACACATTTTGTAGCACATTTTTCTTTTATACTAGTTTGAATAATACTAGCTTT -CAGCAGTCATAAAAAGTAATACTTAGGTGAGATGCGAGGAGAAGTTATCATTGCGTAGAC -CATTTTCTATGTCAATTGAAGAGCCTCTAATATCAGAAAATGTAAAGGTAACTAGTATGC -TTTCCTCTTGGTTTGAGTTCAGCCGAATATGCAACATATGATTGTTGTATAAAGCTTTTC -GTGGAACGGATTTCAATTAAGATCAATTGGATCTCATCAATACTTAACTTATTTGTAAAT -TGTGATCACATGCACATTATCCTTTATATAGGGTGAACATTAGCAGGACTTTTTTTCCCT -TATGCCTATTATTTGGAGAAAGAATATGCCTATCATTATGCCTTGATTAGCAACAGAAAC -AATATGTGATACTTGTTGGTTAATTAATGAGTATCCGGTTGGAGTATTAGCTCATTTATA -GCATGTGTTCCATTATAGTACTAGCTAGTTATTGGCGTGTATACTTGTACACCACTGTCT -CTAAACAACAATCATTATTAAATTCCTGTACATTCTTTCGTCAGGATCAGGACACATCTC -CTAAAAAATCTATACACAACCAATACATTTACTCACAAGATACTTATACAGTTATACCTA -TTTCATATGAGTCACACCAAAAAGATGAATGAAACAAGATATGCATCACGAACTTTGTAG -TTTGTATCGGCATTACATATAGGGCTTTAGCCTTCTATTGAGTAAGTGCCTGAGTTGGAG -ATAATAAGACTTGAACAGTTGATGTTTTCCATGGTTGCAAGAAAAGAATATCTCGTTCTA -TGCTCTGGTGATTGGTGATCTCTAGCTTGCCAGACACGCGAACTCCAGTCATTCTCCAAA -TCATATTCCATGATTCCAAAGAAGCCTATTCATCTATGTTATAAAAGAAGAAGTCTATCC -ATCTATTAGCTTCTCTCGTAGATCCACTGCGGTAAAAAAACCACATGCATTTTCATTGAT -CAATCAAGATAGTTGCCACTACTCCTGAAGGCTAATTCTTGGATCATACAATTCTTGTTT -TTTGTTTCATGCTTTATGCCTTCTCTTTTTTCATAATGGTAGATAAATTGCTAATCATCA -TGAGTTGGATGATAGCCATTACCTAGTTCTCCTTTAATGGTCAAAACCTTTTTGGCTCTG -TTGTCCTCCTTGTTGTCCTATCAATGTTGTTAATCTGCAATTGTGTTGCCTGAATTCTGA -ATATAGAATCTTTTCCTTTTATTAGTTTTGCTGTAATTTTTCTTTCATCTCATAATTCTT -TATCTTGTATCATTTGCAGCTAGAAGAGTTCCGCAAAAAGAAAGCAGAGAAGGCAAAAAA -GTCAACTTCCAATAATCAACCTCATGGTTCGGGTGGAGGCTTTGATAACCAACCTTCAGA -CAGTGAACACACAAGAATCACTGACTCTCGTGGAGCTGGTACATCTGATGCCCTTGATGG -AGCTGTTTCAGAGTTATCTCGAGTAGACGTTACACATGATTTCAAGAATCCTGATCTTGC -ACAGAAGAGTGGTTTCGCTTCTTCCTATGAAGCTAATGCTAGTCCTACTCATAGTTTACA -CAACAATGATAATGATGCTAGCGCTACTTCTACTATTAGTGGAAACAATCATGGTTTTAC -TTCTTCCATCTCCACGCCATCTCATTTTAGAGATAAAGTGCTTAAGGGTGATGAGAAACC -TAAATCATCTGAACAATTCAGTGATAGTTATAATCCCCCTGAGAAGACGGAGAATGATGG -AGCCTTGGGAAGTATTGGATTTGGATTTAATACTAGTCATTCTACACCTAATTTTCTGTC -ATCATTCCCCAGTTACAGTAAATTTTCCGGTTTGTTTAGTCATGATGGTGTAGCTAAAAG -TGAAATAGAGGGAAAAAAAACAAAAGATCTTTCTGTAATGAACTCTAGTACTTCTCATGC -TTTTCCTGCTAATGTTTCACCTGAAAACTCCCGTGGTCCTCATCTGCAAGAAAAACCAGG -TTTTATGGATCGTTGGGCTAGTGGGTTTACCTCCTCATCATATGAAGGTAACTTTATGGT -AATTTGGAGTTCCGTTTTTTCTTTTTTTAATCCTTTATTGTGCTTCCTTTTTACCTTAGA -GAGCCTCATTGCGTACCTGCGATTCATCTATCCAGTTAATTAATTGGGGTTGCATAATCT -GACATCTATTTCCCTTTTTTTTTTGATAGATCATATGCGCCCCACAACCAGCAGTACAAA -GTTTTCTTTGGAAGATGGGCAAAGAGATGGTACTGTTGAAGCTAATAGTTCTATAATTTC -TGATATTGGGTATGGCCAGTTCAACAACTCTGGTTTTTACATGAATAATAATTCGTCTTC -TTGGGCATCTGATTCTAAACATGAGGACATCAGTTCTGAAGCAAGAAGTTCTTCTAGTAA -TTCAAAATTGTCTACAGCCACTGTTGGGAGGAAATCTCGTCCGTCTTTCCTTGATTCCAT -CAACATTTCAAAAGTTCCTGTGGTATCCCCTTCTCCAACTGAATCAGTTTCTGCAGACAG -ATTTGATCCAAAGGGTCATCCCACGGACACTTTGGAATCGTCCAACTCCAGGAACATGAT -GACTTCTTCAACCTTTTCTGCAAGTGGGTCTGATCAGTTGAATCATCATGCTGAGAAAGA -CACGGGGAACATGGACAACCGTTATCAGTCTTTTGCACAAAAACAGAATGAAGATTTTGC -TGCTTTAGAACAGGTTTCTCCACATTTACTTCCCTTGCTTTAGAAAGTGATAAGTTTAGG -TCAGGATGTCTTCAAAGTCAAAATTTAGTTTGAAAGTACTGCTAATTGATGGTTAATATA -TGAAAAGCACTCTGCTGCTTCAGGATAGAAATCAGTCTTTATTAGAATGGAAAACCTTTT -CGTCTTGTTTGGCTTAGTCATTTTAAATTGTCTCGATCAATTGTCCCTTTATGAAGCAAG -TTTTTCTCTGTTCGACTAGGATGTTATGAATCCTTCTTTA diff --git a/probes/mapping/blast/ch12-sc10-3_Product.fasta b/probes/mapping/blast/ch12-sc10-3_Product.fasta deleted file mode 100644 index 698ce8eec9be14fc44c3c3d341a3ac6a0dbd82cf..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/ch12-sc10-3_Product.fasta +++ /dev/null @@ -1,54 +0,0 @@ ->S_lycopersicum_scaffolds.fa_SL2.40sc05380_927120_930266_ch12-sc10-3_Product -GGTGGGTCTGCACGCTATACTCATTGAAATGCTTTACAGCATGAAGTGAGAACAGTAATG -GAATCTTAGCATCTTATTAATGGCTATCTTCTTGCAGTGTTTATGTAGTATCTCTGATGC -TTAAACTCAGTGAAAATTTATAACCTTTTATTTCAGAAGCAGTATTGGCATTGGCATGTA -AATCTTAACAAATTTCTAACTCACATAATGTGCAGGTTCCATATAATGCTCGACATTCGC -CACGTGGCATATTTTGCAGCCGCACATTAAATCTACGATCAATCAGTGCAATTGGATATG -ATATGGACTATACACTGATGCACTATAACGTGATGGTACTTTTTAGTTCTTGTTTCATGT -GATGTAAGCTATTAGCTCATGTTTTCTTTGTTACAAATTGAGGCTAATGTTCATTGGTTA -CACATTTATTTCTTTCATTTGCCACCACATCTATTGTTTGCTTGATTGTTGAATTGCATA -TGACAATGTTGTGCTATAGGGGAACTAATCCTATAAGGCAGCGTAGGCAGTTTTTATCCA -TACATATGTTTTCTTTGTTACTAATCCTTTTATTTTGGTGCCTGATGAAGCTCTTATTTC -ATTTGTATTAAGAGATTAAATTCTGATGATAAGAAAAAGTGCTTTATATGCGTTATCAAA -AAAGAGAAAGTACTCTATTTGCCTTAAATTCGTTTATCTTTTTTTTTGAGTTGAAATATG -ATTTTCCATTTTTATTCTCTTAGATTTTTGTTGGAAGTGCCATGACAGACTATCATTTAG -ACTGTTTAAATTTAAAATACATTGCTGTCTTGTATATTCTTTTTGTCGTCCCTTGAGGAG -CTTTAAATTGTTTTTGTCTTTGGCATATGTTACTGGTGTAGTATGATTTAAGTCCATAAT -TTACAGGCCTGGGAAGGAAGGGCTTATGATTACTGCATGGAGAATCTGAGAAATGTGGGT -TTCCCTGTGGATGGGCTTGCATTTGACCCTGATCTGGTATAGTCTGACCATGTGAGCATG -CTAATGGTTTATTTAATACACATTTGAGGACATTTCATTATAAAACAGGTGATAAGAGGC -CTTGTAATAGACAAAGAGAAAGGTAACCTAGTTAAAGCAGACAGATTTGGATATATCAAG -AGGGCAATGCATGGAACAAGAATGCTTTCAACTCGAGAAGTGAGGTATGGCTTGGGCTTT -TGTGTCTACTTGTCAGCTCAAATATAGATCCATATAACCGTAACTTCTAGCAAAGATTGT -CCACAAAATGTTGCTTTGCAAATTGGGAAATAGAAGCTCACTACACAGCCAAAAGTTTTA -TTTGCTCCATGAAAATTTGAATGAATGTTCTACATTTTGATTTGGAAAATTGGGTAATGT -TTTGGTTAGTGTCTCATATTTTCTATGTTTGGAAGTGAGATCTACGGGAGAGAACTGGTT -GACCTGCGTAAGGAGAGTAAATGGGAGTTCCTGAATACACTATTCTCAGTTTCAGAAGCA -GTGGCTTATATGCAGGTAGATCACTTGGCCTCCCTCAGTATACATGCCATGACTCAATAC -TAAAAGACATTATCTCTTCATGTTTGTCATATACATTTGTTAGTTTTTTTTTCTTGTGAA -GGGATTTGTATTACTTCTATCTCTTCTTGATGCAGTTCCTTTCCTTGTTAAAATAAAATG -TACTGATTTAGTAGGTCGTGACTTGTGGGTTTTCATTATTATTGTTATGTTTCTTTCTTT -AGGTTGAGACATTTTGGTTATCTATTTTATATTCGTTTTAGGTTTTCTCTTGATCATAAG -AAGCACATGCTTTATTACTGAAGTGGTTCTTGTTAACCAAATTTATAGATAGTTGTCTAC -TCCTTTCTGTAGAGGCTGATATTTTGCTTAATTTATTTGGACAGAACGGTTCATCCAGTT -GCCTGTTTCTGATTAATATTGATATTTGAATTGCATAAATTTATTGAACACCTGAGGTTT -CAACTAAAAAGAATGTAATATTGCTTCTTCTGCACTTGCCCTAAATCCTAGACATGTCTC -TTTTGCAGTTGGTAGATAGGCTGGATAAAGGAGTTATAGGACCAGATCTCTGTCCAAATG -AGTATAAAGGACTTTACAAGGTATGGTTGGATGCTGTGTGTGAATGGATTGTGATGTGAA -CATTGAGTTTGCCAACCTTTTTGTATTCTATTTAGGCTGTTGGTAAGGCACTCTTCAGGG -CACATGTAGAAGGCCAGCTGAAGGTATGTGTTTCATTGATCCATTGCTTCACATGCCGGG -AGCTGCAAATATCACTCTAAGCTATTTCACCCATGCAGAGTGAGATAATGTCCAAGCCTG -AATTATTTGTGGAACCTGATCCTGAGCTACCTTTGGCATTATTGGATCAAAAGGAGGTAT -TTCTAACTCTATCCATTTGATTGAATATCAGTCTATTTAGAGCCTTGCATAAGTAATCTT -AATTAATTTAGCATAGCAAGTGTAGAAGTCCAATAGGACATCAATTGGGAGAATAAGTTG -TCCAATTTCTTGTTAAGATTTATGAAGCCCCTATCAAAAAATGATGGCTGATTCAGCATC -TAACATTTCATGTTTTATCAGGCTGGGAAGAGACTTTTACTGATTACAAATTCAGATTAT -CATTACACAGACAAAATGATGCAGCATTCGTTCAATCGGTACCTTCCCAATGATATGAAC -TGGCGAGATCTATTTGAGATGGTGAGTAAGCAGAACAGGATTTTGATAATAGCTAATCAT -TGAAGTCTTTATCTCATAGTGTAATGCTTTTGAACAGAAGTTTATAGAAAAGATAATTTT -GTCAACGCCAAATGTCACTGTTAGAATTTGATGGCTAACTATTTTGACTCCTTTATTGCT -TTCTACAAATTTAAATTTCTCAGTGAAGTGTTAATTTTATCGAAGTGTTGATTGTTAAAT -GACTCCAACCAAATGTATTTTCCTTCTTTACCCAATACAGGTTATAGTCTCAGCTAGGAA -GCCAGAATTCTTCCAAATGGCCCACCCAATGTATGAAGTGGTGACTGGTGAAGGTCTGAT -GCGTCCTTGTTTTAAAGCTCGCCCAGGTGATTAAACTTCTAAACTGATGATAGGAAAGTC -ATCTCTATTTTGGATAAGTAAATGAAA diff --git a/probes/mapping/blast/ch12-sc10-4_Product.fasta b/probes/mapping/blast/ch12-sc10-4_Product.fasta deleted file mode 100644 index 0367714fd4c6d05f0e4635da39666c3844176ef4..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/ch12-sc10-4_Product.fasta +++ /dev/null @@ -1,45 +0,0 @@ ->S_lycopersicum_scaffolds.fa_SL2.40sc05380_369372_371958_ch12-sc10-4_Product -CAAGTACATGGTGTGTAACATCCTCTATTATTCAGATTAATTTTTGTTTAGATGTAAAAA -GAGTGAGGGTTATTTGTTGCTGAATGAGTGAAGTTCTTTTTGCCATGTCTAATACCACTT -CTACTCAGCATTGTACTTCATTTTCAAGTTTTTATGCTTGAGCATGCATCTTTTTTTTTG -GTTTTTGCATCTCATTGTGGATTCTTAAAGTGTAGTTTAGTGTCTAATACAGAGAGTTGC -TGACTTTTACTTTCATATTAATGTTTGTCAGACCCTATATATTCTGGAGAACCTGTTCCA -GATCTTACACCAGATTTCACTAAAGTCGACAAGCGATCCAATTCATGCATAGTAAGTGGA -TCTTGTGCAACTTGATCTTAGTGATTTGGTAAACTTTGATTTCATAGTTCTCAACCATGA -ACTTACTGCATTATATACAGGAGTGCTTGATTTGTGTCAAGTTGATAATTAATTGAATTT -AGACTAGGAATTTTATGTATATCGTTTACTCTTGTGACAACAGTTGCTGATATACTTCAG -TCAACTGATCTTTTAAATGAATAATGTGAAGGAAGTACCAATCATAGAACTGTGGTATAG -CAACACTACACAAAAGAATCATGTAGGGCTATTAATTTGAACTTCTCTTTTGTTTAGATA -TTTTGCATTGGACCATGGATATACCTTTTTTAAAAAAGAATCATCCACCGTGGAGGAAAA -CTTGTTTTAGCGAGACCTTACCTATCTCGAGGTTTTAAATATCTTTACATTTTTCTACTG -GCTCAAATGTGAATGGGTTGAGATAAAATTGTGCTTTATTTAGTGCCTCCTGCCCTACCA -TATCTAGATCTTACAATCAAGGTTAAAGCACTTAAGTCAATCTGTTGAATTACCTACTCT -GCTTTTACATTGGTCCAATAGGGGTATGGATCCATTTCCAAGATAAACTCTCATGGCTCT -GATTTGGATGGTGCAAACTTAAAAAAGTCAAACAAGTCTTCTCATCCTGAATATTACATC -AACCAAAAGCCTGATCGGAATTCCTCTATGCACAATGGTGATCGGTACTATCTTGGGCGG -AACTCGTCGATAGAGATGCGCAAAGATTCTGGAAGAGAAGTGGCAGTTGATGGCAGATGC -AACTATAAGCTTATGGCTAAACATGATGGTGCAGCCAATCCTGGCTCTAGTGGTGGTTTT -CAAAGTTCCTACATTGGAAAAGTCAACAGGGAGCAGGTGACTGCTAGGTTCACTAGCCGT -GATGGCTTGAGCCTTGACATTGCGGAGGAGGAAGATCTTCAATGCAAGCCTTCAAATTTT -GTCCATAAGGGAAGTAAGCAACATTATTGTCCAGAGAGAGAGCTCTCCAGTACAGTTGAA -AAGGTATAATGCCATTCTTGTGCTGTGCTTCTTTGTTATCCAGCTATATCTAGATAATTT -TACCTTGATTGTGATATATAGGATTACATCCATGTGGACCGACCAACCGTTGATGAAGAT -TATAATGAAGATCATGTGAAGATACAGTGGGAGAAGGAAATGAGGGTAAGCTTTTCAGCT -CATGTTAGTATGTTACTATTTGTAATTCCTTTAGATAAAGATATGGTCATTTGAACTCTT -TGAATACGAAATATTTTGAAGGTTGCCAAAAGAGCAACGGATGAGGAAGCTCCTAACCAT -CAAGAGTATGTGAGGAAAGCATCAGTGACTAGAATGCCATCCCAGACAAATCATCAGATA -AGGTTTGGCCATGTTTAAGACCTTGGTTTCTAATCTAATGTGCATCTATATTTGAACGTA -TATGGCTCTATCTTGAGATGTTTGACTGAGATATCAAGGTTTTGGAGAATCATATTTAGT -TCAATGGCTTTTGCTGAAACAATTTTAAAGATAGATTTGTGATGTAAAGTACAGAAGAAT -GCATGGTAGAAAGTTCTGCCTCTCATAAGTGATTTATGTCTCCTGTCTCCAACTCCATTA -CCTTGTCTTGTGCATTCATAGTAGGTTTACTTATGACACTTCTGAACAACGTACGGTCCT -CTGTACATTGTGCATAGCATAGTGTTCAAACACAAACATTTGTAGCCATTACTGAGTGTG -TCAAGTTCTGCTGTCTTGTATTTGTCGGTGTGATAGTAAAGATGTGAAGAATGTCTTTTA -CCTTCTATATATGACAAAAGTGAAACTAGTAACCTGAAATGACTGGTTCCGATAATGTGA -ATTATTTGCAATGCTGATGTATATAAGTTAAATGTTTTTAACAATTGTCTTCATTGTTAT -GCTAACAATGATACTCTCTGTGTTCGTTCTAGTTTTGCTGCAGAGATGTCATCTAGCTTT -AGTGAAGATGACAAAACAGAAGAAACCAGTTCTTTTGAGGATTGAGAGATTTACAGTTTC -CAGAGAAAAGTTAAAAAGTGCAGAAGCTGTAGTGATTCTTGAATTCCTATTTGTTGATAG -CTTAAGTTACTTTGGATTTGTACAGTTCAAAACAACTTATAATGCTCTCATCAGTACACC -AGCATGTGAAATTGAACAACTTTGGTCTCTGTACAGTAAAAGTAGTAGTACTTTTTTTTA -AAATGTA diff --git a/probes/mapping/blast/pos b/probes/mapping/blast/pos deleted file mode 100644 index aed1425186831c6e0fcfec3f77dad1c4bdb9a009..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/pos +++ /dev/null @@ -1,43 +0,0 @@ -function cutFasta { - NAME=$1 - SCAF=$2 - START=$3 - END=$4 - fastaCut.pl ../../data/S_lycopersicum_scaffolds.fa $SCAF $START $END ${NAME}_Product > ${NAME}_Product.fasta -} - -cutFasta ch12-sc02-1 SL2.40sc04878 622710 624594 -#LENGTH=1884 - -cutFasta ch12-sc02-2 SL2.40sc04878 3080728 3082538 -#LENGTH 1810 -cutFasta ch12-sc02-3 SL2.40sc04878 4093931 4095019 -#LENGTH 1088 - -cutFasta ch12-sc03-1 SL2.40sc04057 3198454 3200936 -#LENGTH 2482 -cutFasta ch12-sc03-2 SL2.40sc04057 7835794 7838398 -#LENGTH 2604 -cutFasta ch12-sc03-3 SL2.40sc04057 13401063 13403730 -#LENGTH 2667 -cutFasta ch12-sc03-4 SL2.40sc04057 22823181 22827553 -#LENGTH 4372 -cutFasta ch12-sc03-5 SL2.40sc04057 23797776 23801944 -#LENGTH 4168 - -cutFasta ch12-sc09-1 SL2.40sc05611 353222 355021 -#LENGTH 1799 -cutFasta ch12-sc09-2 SL2.40sc05611 528593 530597 -#LENGTH 2004 -cutFasta ch12-sc09-4 SL2.40sc05611 967164 970727 -#LENGTH 3563 - -cutFasta ch12-sc10-1 SL2.40sc05380 1864775 1867879 -#LENGTH 3104 -cutFasta ch12-sc10-2 SL2.40sc05380 1423814 1427393 -#LENGTH 3579 -cutFasta ch12-sc10-3 SL2.40sc05380 927120 930266 -#LENGTH 3146 -cutFasta ch12-sc10-4 SL2.40sc05380 369372 371958 -#LENGTH 2586 - diff --git a/probes/mapping/blast/res b/probes/mapping/blast/res deleted file mode 100644 index 4ac938f4bc70b352aa35bc61353e9c379f846dc5..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/res +++ /dev/null @@ -1,30 +0,0 @@ ------------------------------------------------------------------------------------------------------- -SEQUENCE LENGTH QRY IDENTITIES GAPS STRAND START QRY END QRY START HIT END HIT CHR ------------------------------------------------------------------------------------------------------- -JBPP0904F 1080 916/929 6/929 Plus / Plus 45 973 62702526 62703448 12 -JBPP0904R 1046 943/965 3/965 Plus / Minus 12 975 62705998 62705036 12 -JBPPH036P06F 1272 321/343 1/343 Plus / Plus 50 392 16714832 16715173 12 - 78 / 88 1/ 88 Plus / Minus 50 137 40283057 40282971 06 -JBPPH036P06R 1182 824/850 7/850 Plus / Minus 6 854 16716635 16715792 12 - 192/223 Plus / Plus 253 475 58123364 58123586 03 - 138/162 Plus / Plus 551 712 58123686 58123847 03 - 151/175 1/175 Plus / Plus 542 716 40281038 40281211 06 - 178/214 Plus / Plus 253 466 40280757 40280970 06 -JBSC0201F 1120 360/362 1/362 Plus / Plus 48 409 16714833 16715193 12 - 79 / 87 1/ 87 Plus / Minus 48 134 40283056 40282971 06 -JBSC0201R 1161 766/776 Plus / Minus 17 792 16716621 16715846 12 - 192/223 Plus / Plus 249 471 58123364 58123586 03 - 138/162 Plus / Plus 547 708 58123686 58123847 03 - 151/175 1/175 Plus / Plus 538 712 40281038 40281157 06 - 178/214 Plus / Plus 249 462 40280757 40280970 06 ------------------------------------------------------------------------------------------------------- - - ------------------------------------------------------------------------------------------------------- -SEQUENCE START FWD END FWD START REV END REV DISTANCE (START REV - START FWD) ------------------------------------------------------------------------------------------------------- -JBPP0904 62702526 62703448 62705998 62705036 3472 -JBPPH036P06 16714832 16715173 16716635 16715792 1803 -JBSC0201 16714833 16715193 16716621 16715846 1788 ------------------------------------------------------------------------------------------------------- - diff --git a/probes/mapping/blast/run b/probes/mapping/blast/run deleted file mode 100644 index 0a49a403415f3b46d4d8ed843593c638798a53da..0000000000000000000000000000000000000000 --- a/probes/mapping/blast/run +++ /dev/null @@ -1,86 +0,0 @@ -DBFASTA=../../data/S_lycopersicum_chromosomes.fa -DBNAME=tomato - -if [[ ! -f "db/tomato.nsq" ]]; then - echo MAKING DATABASE - formatdb -t $DBNAME -n db/$DBNAME -V -p F -i $DBFASTA -fi - - - -function runBlast { - INFASTA=$1 - PAR=$@ - - if [[ ! -f "$INFASTA.blast" ]]; then - echo "RUNNING $INFASTA" - CMD="blastn -outfmt 2 -evalue 1e-1 -db db/$DBNAME -out $INFASTA.blast -query ${PAR}" - echo " CMD $CMD" - eval $CMD - else - echo "SKUPPING $INFASTA. EXISTS" - fi -} - - -OPTS='-gapopen 2 -gapextend 1 -num_threads 40 -word_size 6' - -runBlast 1_primers.fasta -runBlast 2_sequences.fasta -runBlast JBPP0904_Product.fasta $OPTS -runBlast JBSC0201_Product.fasta $OPTS -runBlast ch12-sc02-1_Product.fasta $OPTS -runBlast ch12-sc02-2_Product.fasta $OPTS -runBlast ch12-sc02-3_Product.fasta $OPTS -runBlast ch12-sc03-1_Product.fasta $OPTS -runBlast ch12-sc03-2_Product.fasta $OPTS -runBlast ch12-sc03-3_Product.fasta $OPTS -runBlast ch12-sc03-4_Product.fasta $OPTS -runBlast ch12-sc03-5_Product.fasta $OPTS -runBlast ch12-sc09-1_Product.fasta $OPTS -runBlast ch12-sc09-2_Product.fasta $OPTS -runBlast ch12-sc09-4_Product.fasta $OPTS -runBlast ch12-sc10-1_Product.fasta $OPTS -runBlast ch12-sc10-2_Product.fasta $OPTS -runBlast ch12-sc10-3_Product.fasta $OPTS -runBlast ch12-sc10-4_Product.fasta $OPTS - - - -./blast2align.pl JBPP0904_Product.fasta.blast -./blast2align.pl JBSC0201_Product.fasta.blast -./blast2align.pl ch12-sc02-1_Product.fasta.blast -./blast2align.pl ch12-sc02-2_Product.fasta.blast -./blast2align.pl ch12-sc02-3_Product.fasta.blast -./blast2align.pl ch12-sc03-1_Product.fasta.blast -./blast2align.pl ch12-sc03-2_Product.fasta.blast -./blast2align.pl ch12-sc03-3_Product.fasta.blast -./blast2align.pl ch12-sc03-4_Product.fasta.blast -./blast2align.pl ch12-sc03-5_Product.fasta.blast -./blast2align.pl ch12-sc09-1_Product.fasta.blast -./blast2align.pl ch12-sc09-2_Product.fasta.blast -./blast2align.pl ch12-sc09-4_Product.fasta.blast -./blast2align.pl ch12-sc10-1_Product.fasta.blast -./blast2align.pl ch12-sc10-2_Product.fasta.blast -./blast2align.pl ch12-sc10-3_Product.fasta.blast -./blast2align.pl ch12-sc10-4_Product.fasta.blast - - - -#G5 OPEN -#E2 EXTEND -#W11 WORDSIZE - -#HTML -T -#-m alignment view options: -#0 = pairwise, -#1 = query-anchored showing identities, -#2 = query-anchored no identities, -#3 = flat query-anchored, show identities, -#4 = flat query-anchored, no identities, -#5 = query-anchored no identities and blunt ends, -#6 = flat query-anchored, no identities and blunt ends, -#7 = XML Blast output, -#8 = tabular, -#9 tabular with comment lines - diff --git a/probes/mapping/bwa.sh b/probes/mapping/bwa.sh deleted file mode 100755 index 4e9be554767c5774a3a22f4de27f6e22b4b051ad..0000000000000000000000000000000000000000 --- a/probes/mapping/bwa.sh +++ /dev/null @@ -1,367 +0,0 @@ -#!/bin/bash - -export BWAFOLDER=bwa -export RAWINFOLDER=raw -export OUTFOLDER=out -export RAWOUTFOLDER=bwa -export MAPEXTENSION=sam -export INFOLDER=../data -export INFASTA=S_lycopersicum_chromosomes.fa -export DBFASTAFILE=S_lycopersicum_chromosomes.fa -export DBNAME=S_lycopersicum_chromosomes -export CORES=40 - -export INFASTQFOLDER=/mnt/nexenta/aflit001/nobackup/Data/Heinz/Heinz_Illumina/ -export INFASTQFOLDER2=/home/aflit001/temptive/probes/mapping/data2/ - -export BWATHREADS=80 -export BWAALN_MAXEDIT=0.04 #-n -export BWAALN_MAXGAPOPEN=1 #-o -export BWAALN_MAXGAPEXT=-1 #-e -export BWAALN_MAXEDITSEED=2 #-k -export BWAEXP_MAX=3 #-n - -mkdir $BWAFOLDER &>/dev/null -mkdir $RAWINFOLDER &>/dev/null -mkdir $OUTFOLDER &>/dev/null - -set -o pipefail -set -e - -LC_ALL=C -SCRIPT_NAME=`basename ${BASH_SOURCE}` - -function echoMsg () { - SEC=$1 - NAM=$2 - PIP=$3 - LNO=$4 - DSC=$5 - shift; shift; shift; shift; shift - MSG=$@ - printf "[%-20b :: pid %05d :: ln %04d (%06ds)%b] %s\n" "$NAM" "$PIP" "$LNO" "$SEC" "$DSC" "$MSG" | tee -a err.log - #echo "[$SEC :: $NAM :: $LNO$DSC] $MSG" | tee -a err.log -} - - -export DSC=" :: FASTQ" - -echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" "CHECKING INPUT FASTQ FOLDER '$INFASTQFOLDER'" -if [[ ! -d "$INFASTQFOLDER" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" "NO INPUT FASTQ FOLDER FOUND '$INFASTQFOLDER'" - exit 1 -fi - - -echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" "GETTING INPUT FASTQ FILES" -export INFASTQ=`find $INFASTQFOLDER -type f -name '*.fastq' -printf "%p "` -echo "$INFASTQ" -if [[ -z "$INFASTQ" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" "NO FASTQ FOUND '$INFASTQ'" - exit 1 -fi -echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" "FASTQ FOUND: $INFASTQ" - - - -echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" "GETTING INPUT FASTQ2 FILES" -export INFASTQ2=`find $INFASTQFOLDER2 -type f -name '*n.fastq' -printf "%p " | grep -P '[1|2|n].fastq'` -echo "$INFASTQ2" -if [[ -z "$INFASTQ2" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" "NO FASTQ FOUND '$INFASTQ2'" - exit 1 -fi -echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" "FASTQ FOUND: $INFASTQ2" - - - -echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" "GETTING INPUT FASTQ2 FILES" -export INFASTQ3=`find $INFASTQFOLDER2 -type f -name '*[1|2].fastq' -printf "%p " | grep -P '[1|2|n].fastq'` -echo "$INFASTQ3" -if [[ -z "$INFASTQ3" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" "NO FASTQ FOUND '$INFASTQ3'" - exit 1 -fi -echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" "FASTQ FOUND: $INFASTQ3" - -BASENAME="$OUTFOLDER/${INFASTA}_$DBNAME" - -echo $INFASTQ -echo $INFASTQ2 -echo $INFASTQ3 -echo $BASENAME - -export DSC=" :: BWA INDEX" -OUT="$BWAFOLDER/$DBNAME.pac" -export DB=$OUT -export DBNAMEFULL=$BWAFOLDER/$DBNAME -CMD="bwa index -p $DBNAMEFULL -a is $INFOLDER/$DBFASTAFILE" -echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " RUNNING BWA INDEX" -echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " DB NAME FULL $DBNAMEFULL" - -if [[ ! -s "$OUT" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " RUNNING '$CMD'" - eval time "$CMD" 2>&1 | tee -a err.log - wait ${!} - if [[ ! -s "$OUT" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " *** ERROR CREATING $OUT :: CMD $CMD ***" - rm $BWAFOLDER/${DBNAME}* &> /dev/null - exitAll "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" - else - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " $OUT CREATED" - fi -else - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " $OUT EXISTS. SKIPPING" -fi - - - - - - - - -export DSC=" :: BWA ALN" -OUT="$BASENAME.sai" -export BWASAI=$OUT -CMD="bwa aln $DBNAMEFULL -t $BWATHREADS -n $BWAALN_MAXEDIT \ - -o $BWAALN_MAXGAPOPEN -e $BWAALN_MAXGAPEXT -k $BWAALN_MAXEDITSEED $INFASTQ > $OUT" - -echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " RUNNING BWA MAP" - -if [[ ! -s "$OUT" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " RUNNING '$CMD'" - #twit.py finished bowtie-build \| starting bowtie $OUT - eval $CMD | tee -a err.log - # 2>&1 | tee -a err.log - wait ${!} - if [[ ! -s "$OUT" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " *** ERROR CREATING $OUT :: CMD $CMD ***" - rm ${OUT} &> /dev/null - exitAll "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" - else - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " $OUT CREATED" - fi - #twit.py finished bowtie \| starting filtering -else - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " $OUT EXISTS. SKIPPING" -fi - - -export DSC=" :: BWA SAMSE" -export BWAEXP_MAX=1000 #-n -OUT="${BASENAME}.sam" -export BWASAM=$OUT -CMD="bwa samse -n $BWAEXP_MAX $DBNAMEFULL $BWASAI $INFASTQ $INFASTQ2> $OUT" - -echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " RUNNING BWA EXPORT SAM" - -if [[ ! -s "$OUT" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " RUNNING '$CMD'" - #twit.py finished bowtie-build \| starting bowtie $OUT - eval time $CMD 2>&1 | tee -a err.log - wait ${!} - if [[ ! -s "$OUT" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " *** ERROR CREATING $OUT :: CMD $CMD ***" - rm ${OUT} &> /dev/null - exitAll "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" - else - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " $OUT CREATED" - fi - #twit.py finished bowtie \| starting filtering -else - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " $OUT EXISTS. SKIPPING" -fi - - - - -export DSC=" :: BWA-SW" -OUT="${BASENAME}_2.sam" -export BWASW=$OUT -CMD="bwa bwasw $DBNAMEFULL -t $BWATHREADS -n $BWAALN_MAXEDIT \ - -o $BWAALN_MAXGAPOPEN -e $BWAALN_MAXGAPEXT -k $BWAALN_MAXEDITSEED $INFASTQ3 > $OUT" -CMD="bwa bwasw -t $BWATHREADS $DBNAMEFULL $INFASTQ2 > $OUT" - -echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " RUNNING BWA MAP :: $OUT" -if [[ ! -s "$OUT" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " RUNNING '$CMD'" - #twit.py finished bowtie-build \| starting bowtie $OUT - eval $CMD | tee -a err.log - # 2>&1 | tee -a err.log - wait ${!} - if [[ ! -s "$OUT" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " *** ERROR CREATING $OUT :: CMD $CMD ***" - rm ${OUT} &> /dev/null - exitAll "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" - else - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " $OUT CREATED" - fi - #twit.py finished bowtie \| starting filtering -else - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " $OUT EXISTS. SKIPPING" -fi - - - - - -export DSC=" :: CONV2POS" -OUT="$BASENAME.pos" -export MAPPINGOUT_POS=$OUT -CMD="perl -nae 'chomp; next if (index(\"@\", \ $F[0]) == 0); \ - \$size = length(\$F[9]); \ - my \$mm = 1; if (\$F[1] & 16) { \$mm = -1; } else { \$mm = 1; } \ - \$begin = \$F[3]; \$end = (\$F[3] + ( \$size * \$mm ) - 1); \ - if ( \$begin > \$end ) { \$t = \$end; \$end = \$begin, \$begin = \$t }; \ - print \"\$begin\t\$end\t\$F[2]\t\$F[1]\t\$size\t\",(\$mm == 1 ? 'fwd' : 'rev'),\"\n\" \ - if (substr(\$F[0],0,1) ne \"\@\")' \ - $BWASAM $BWASW > $OUT" -ERRMSG="ERROR CREATING $OUT :: CHR $CHROMNAME :: SCA $SCAF :: $CMD" - -echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " GENERATING RANGES FOR CHROMOSSOME $CHROMNAME SCAFFOLD $SCAF" - -if [[ ! -s "$OUT" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " RUNNING '$CMD'" - - eval time "$CMD" 2>&1 | tee -a err.log - RES=$? - wait ${!} - if [[ $RES -ne "0" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " *** $ERRMSG :: EXIT WITH ERROR: $RES ***" - rm ${OUT2} &> /dev/null - rm ${OUT} &> /dev/null - exitAll "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" - elif [[ ! -s "$OUT" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " *** $ERRMSG :: COULD NOT FIND OUTPUT FILE ***" - rm ${OUT2} &> /dev/null - rm ${OUT} &> /dev/null - exitAll "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" - else - DID=$((DID+1)) - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " $OUT CREATED" - fi -else - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " $OUT EXISTS. SKIPPING" -fi - - - - - -export DSC=" :: MKLIST" -OUT="$MAPPINGOUT_POS.list" -export MAPPINGOUT_POS_LIST=$OUT -CMD="gawk '{print \$3}' $MAPPINGOUT_POS | perl -ne 'BEGIN{ %n = (); } END{ print join(\"\n\", sort keys %n)} chomp; next if (\$_ eq \"*\"); \$n{\$_} = \"\"' > $OUT" - -echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " GENERATING LIST FOR $MAPPINGOUT_POS TO $OUT" - -if [[ ! -s "$OUT" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " RUNNING '$CMD'" - - eval time "$CMD" 2>&1 | tee -a err.log - wait ${!} - if [[ ! -s "$OUT" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " *** ERROR CREATING $OUT :: $MAPPINGOUT_POS :: CMD $CMD ***" - rm ${OUT} &> /dev/null - exitAll "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" - else - DID=$((DID+1)) - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " $OUT CREATED" - fi -else - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " $OUT EXISTS. SKIPPING" -fi - - - - - - - - - - - - - - -for chr in `cat $MAPPINGOUT_POS_LIST`; do - export DSC=" :: $chr :: FILTER POS THROUGH LIST" - OUT="$MAPPINGOUT_POS.$chr.pos" - export MAPPINGOUT_POS_CHR=$OUT - - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " GENERATING LIST FOR $MAPPINGOUT_POS_CHR CHR $chr TO $OUT" - - if [[ ! -s "$OUT" ]]; then - CMD="grep $chr $MAPPINGOUT_POS > $OUT" - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " RUNNING '$CMD'" - - eval time "$CMD" 2>&1 | tee -a err.log - wait ${!} - if [[ ! -s "$OUT" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " *** ERROR CREATING $OUT :: $MAPPINGOUT_POS_LIST :: CMD $CMD ***" - rm ${OUT} &> /dev/null - exitAll "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" - else - DID=$((DID+1)) - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " $OUT CREATED" - fi - else - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " $OUT EXISTS. SKIPPING" - fi - - - export DSC=" :: $chr :: MAKE COVERAGE" - OUT="$MAPPINGOUT_POS_CHR.cov" - export MAPPINGOUT_POS_CHR_COV=$OUT - CMD="cat $MAPPINGOUT_POS_CHR | ../range > $OUT" - ERRMSG="ERROR CREATING $OUT :: CHR $chr :: $CMD" - - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " GENERATING RANGES FOR CHROMOSSOME $chr to $MAPPINGOUT_POS_CHR_COV" - - if [[ ! -s "$OUT" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " RUNNING '$CMD'" - - eval time "$CMD" - RES=$? - wait ${!} - if [[ $RES -ne "0" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " *** $ERRMSG :: EXIT WITH ERROR: $RES ***" - rm ${OUT2} &> /dev/null - rm ${OUT} &> /dev/null - exitAll "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" - elif [[ ! -s "$OUT" ]]; then - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " *** $ERRMSG :: COULD NOT FIND OUTPUT FILE ***" - rm ${OUT2} &> /dev/null - rm ${OUT} &> /dev/null - exitAll "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" - else - DID=$((DID+1)) - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " $OUT CREATED" - fi - else - echoMsg "$SECONDS" "$SCRIPT_NAME" "$$" "$LINENO" "$DSC" " $OUT EXISTS. SKIPPING" - fi - - export MAPPINGOUT_POS_CHR_COV_SMOOTH="$MAPPINGOUT_POS_CHR_COV.smooth.cov" - if [[ ! -s "$MAPPINGOUT_POS_CHR_COV_SMOOTH" ]]; then - cat "$MAPPINGOUT_POS_CHR_COV" | ../add_smooth_colums.pl > $MAPPINGOUT_POS_CHR_COV_SMOOTH - fi - - export MAPPINGOUT_POS_CHR_COV_SMOOTH_IMG="$MAPPINGOUT_POS_CHR_COV_SMOOTH.png" - if [[ ! -s "$MAPPINGOUT_POS_CHR_COV_SMOOTH_IMG" ]]; then - ../mkplot.pl --input=$MAPPINGOUT_POS_CHR_COV_SMOOTH - fi - - - - echo - echo - echo - echo -done - - - -