Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006954.1 Corchorus capsularis cultivar CVL-1 contig06975, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 78777
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1934 original size:977 final size:970
Alignment explanation
Indices: 1--6299 Score: 6100
Period size: 977 Copynumber: 6.5 Consensus size: 970
*
1 AAAAACCTTTCTTTTCTTTTTTGCGTTGAATTGTCTA-TTTTTCTGACTATTGTGGTAAAAAAAA
1 AAAAACCTTTC-TTTCTTTTTTGCGTTGAATTGTATATTTTTTCTGACTATTGTGG-AAAAAAAA
65 TTGAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTTTATCCGAAATCGTTTACTAATCACGGT
64 TTGAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTTTATCCGAAATCGTTTACTAATCACGGT
** *
130 TTATGATTATAAACGCGTTCCAGGTTCCCGGCTCAGTTTTGCAAGATTTTTGACGCAAAGACTCC
129 TTATGATTATAAACGCGTTCCAGGGCCCCGGCTCAATTTTGCAAGATTTTTGACGCAAAGACTCC
* * *
195 TTGAAATATCTATTTTTATTGAACCAAATCTCAGCCATATCGGATATAAGGATGTTTTTTCGAGC
194 TTGAAATATCTATTTTCATTGAACCAAATCTCAGCCATATTGGATATAAGGATTTTTTTTCGAGC
* * * *
260 ATATCAATCTTGTTTCGATTTAATTAGGAATTAATTCGGAAAAAAAAATGGAAAAAACCATAATA
259 ATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGG--AAAAAAATGG-AAAAACGATATTA
* * * *
325 GAAGCGTGAAAAGCCCGTAAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTTTTGTGTCA
321 GAAGCGTGAAAAGCCCATCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGACA
* *
390 AAAAATTAAGAAAAAACTTTTCTGGTAAGTTTTTAGCAAATATCGTGTACTAACCATCACTGCTT
386 AAAAATTAAGAAAAAACTTTTC-GGTCAGTTTTTAGCAAA-ATCGTGTACTAACCATCAC-GGTT
*
455 TTGGCTAAAAACGCGTTCCCGAGCCCCGGCTCAATTTTGCATAATTTTTGGCGCAAAAACTCCTT
448 TTGGCTAAAAACGCGTTCCCGAGCCCCGACTCAATTTTGCATAATTTTTGGCGCAAAAACTCCTT
* * * * * *
520 GAAATATGTATATTTATTGAACCAAATGTCAGCCACACTGGATATAAGGATATGTTTTTACGAGC
513 GAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGC
* * *
585 ATCTGAATCCTGTTTCGTTTTAATTAGAAATTAATTCGGAAAAAAATTTGGAAAAATGATATTAG
578 ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAA-ATGGAAAAATGATATTAG
*
650 AAGCATGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTATGGCAA
642 AAGCATGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAA
*
715 AAAATTGTAAAGAAATAATTTCGGGTCAGTTTTCATCCGAAATCGTGTACTAATCATCACGGTTT
707 AAAATTGTAAAGAAATAATTTCGGGTCAGTTTTCATCCGAAATCGTGTACTAACCATCACGG-TT
* * * * * **
780 TTTGGTTAAAAAACGCATTTCGAGGCCCCGGCTCAGTTTTAAATGAATTTTGGCAGGGAGACTCC
771 TTTGGCT-AAAAACGCGTTTCGAGGCCCCGGCTCAATTTTGAATGATTTTTGGCAGAAAGACTCC
* *
845 TTGAAATATCTATATTCATCTAACCAAATCTCGGCCACATTAGATTTAAGGATTTTTTTTACGAG
835 TTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATATAAGGATTTTTTTTACGAG
*
910 CATCTAAATATTGTTTCGATTTAATTAGAAATAAATT-GTAAAAAAATGGAATAAGCATATTTAA
900 CATCTAAATATTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGAATAAGCATATTTAA
974 AGTGAG
965 AGTGAG
*
980 AAAAACCTTTCTTTTCTTTTTTGCGTTGAATTGTCTATTTTTTCTGACTATTGTGGTAAAAAAAA
1 AAAAACCTTTC-TTTCTTTTTTGCGTTGAATTGTATATTTTTTCTGACTATTGTGG-AAAAAAAA
1045 TTGAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTTTATCCGAAATCGTTTACTAATCACGGT
64 TTGAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTTTATCCGAAATCGTTTACTAATCACGGT
*
1110 TTATGATTATAAACGCGTTCCAGGGCCCCGGCTCAGTTTTGCAAGATTTTTGACGCAAAGACTCC
129 TTATGATTATAAACGCGTTCCAGGGCCCCGGCTCAATTTTGCAAGATTTTTGACGCAAAGACTCC
*
1175 TTGAAATATCTATTTTCATTGAACCAAATCTCAGCCATATCGGATATAAGGATTTTTTTTCGAGC
194 TTGAAATATCTATTTTCATTGAACCAAATCTCAGCCATATTGGATATAAGGATTTTTTTTCGAGC
* * * *
1240 ATATCAATCTTGTTTCGATTTAATTAGGAATTAATTCGGAAAAAAATGGAAAAACCATAATAGAA
259 ATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAA
* *
1305 GCGTGAAAAGCCCGTCAATATTTTTGGCGTTGAATTATATATTTTTTCTAAGTATTGTGACAAAA
324 GCGTGAAAAGCCCATCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGACAAAA
* * * * *
1370 AATTAAGAAAAAACTTTTCTGGTAAGTTTTTAGCAAAAACCGTGTACTAATCATCTCTGCTTTTG
389 AATTAAGAAAAAACTTTTC-GGTCAGTTTTTAGC-AAAATCGTGTACTAACCATCAC-GGTTTTG
1435 GCTAAAAACGCGTTCCCGAGCCCCGACTCAATTTTGCATAATTTTTGGCGCAAAAACTCCTTGAA
451 GCTAAAAACGCGTTCCCGAGCCCCGACTCAATTTTGCATAATTTTTGGCGCAAAAACTCCTTGAA
* * * * * * * * *
1500 ATATGTACATTTATCGAACCAAATTTCAACCAAACTGGAAATAAGGTTTTGTTTTTACGAGCATC
516 ATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATC
* * *****
1565 TGAATCCTGTTTCGTTTTAATTAGAAATTAATTCGGAAATTTTTTTTGGAAAAATGAT-TTAGAA
581 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAA--AAAAATGGAAAAATGATATTAGAA
* *
1629 GCATGAAAAGACCATCAATCTTTTTGTTGTTGAATTATATATTTTTTCTGAGTATTATGGCAAAA
644 GCATGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAA
* *
1694 AATTGTAAAGAAATAATTTCGGGTCAGTTTTCATCCGAAATTGTGTACTAATCATCACGGTTTTT
709 AATTGTAAAGAAATAATTTCGGGTCAGTTTTCATCCGAAATCGTGTACTAACCATCACGG-TTTT
* * * **
1759 TGGCTAAAAAACGCATTTCGAGGCCCCGGCTCAGTTTTAAATGATTTTTGGCAGGGAGACTCCTT
773 TGGCT-AAAAACGCGTTTCGAGGCCCCGGCTCAATTTTGAATGATTTTTGGCAGAAAGACTCCTT
* * *
1824 GAAATATCTATATTCATCTAACCAAATCTCGGCCACCTTAGATTTAAGGATTTTTTTTACGAGCA
837 GAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATATAAGGATTTTTTTTACGAGCA
*
1889 TCTAAATATTGTTTCGATTTAATTAGAAATAAATT-GTAAAAAAATGGAATAAGCATATTTAAAG
902 TCTAAATATTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGAATAAGCATATTTAAAG
1953 TGAG
967 TGAG
* * *
1957 AAAAAGCTTTCTTT-TTTTTTGCATTGAATTGTCTATTTTTTCTGACTATTGTGGTAAAAAAAAT
1 AAAAACCTTTCTTTCTTTTTTGCGTTGAATTGTATATTTTTTCTGACTATTGTGG-AAAAAAAAT
*
2021 TGAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTTTATCCGAAATCGTTTACTCATCACGGTT
65 TGAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTTTATCCGAAATCGTTTACTAATCACGGTT
* * * *
2086 TATGATTATAAACGCGTTCCAGAGCCCCGGCTTAGTTTTGCAAGATTTTTGACGTAAAGACTCCT
130 TATGATTATAAACGCGTTCCAGGGCCCCGGCTCAATTTTGCAAGATTTTTGACGCAAAGACTCCT
* * * * * * *
2151 TGAAATATCTATATTCATCGAATCAAATCTCAGCAATATAGGATATAAGAATTTCTTTTTTTGAG
195 TGAAATATCTATTTTCATTGAACCAAATCTCAGCCATATTGGATATAAGGA-TT-TTTTTTCGAG
* *
2216 CATCTCAATCTTGTTTCGACTTAAATAGAAATTAATTCGGAAAAAAAAATGGAAAAACGATATTA
258 CATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGG--AAAAAAATGGAAAAACGATATTA
** ** * *
2281 GAAGCGTGAAAAGCATATCAA-ATTTTTTGGCGTCCAATTATATACTTTTTCTGAGTATTGTGCC
321 GAAGCGTGAAAAGCCCATCAATA-TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGAC
* * *
2345 AAAAAGTTGAGAAAAAACTTTTCGAGTCAGTTTTTAGTCGAAATCGTGTACTAACCATCACGGTT
385 AAAAAATTAAGAAAAAACTTTTCG-GTCAGTTTTTAG-CAAAATCGTGTACTAACCATCACGG-T
** * ** * *
2410 TTTAACTAAAAATGCGTTCAGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCT
447 TTTGGCTAAAAACGCGTTCCCGAGCCCCGACTCAATTTTGCATAATTTTTGGCGCAAAAACTCCT
* * * * * *
2475 TGAAATATCTATTTTCATTGAACCAAATCTCAGCCATATCGGATATAATGA-TT-TTTTTCCGAG
512 TGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAG
* * * ** *
2538 CGTCTCAATCTTGTTTCGATTTAATTAGGAATTAATTCGGAAAAAAAATGGAAAAACCATAATAG
577 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAATGATATTAG
* * * * *
2603 AAGCGTGAAAAGCCCGTCAATATTTTTGGCGTTGAATTATATATTTTTTTCTGAGTATTGTGGCA
642 AAGCATGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATA-TTTTTTCTGAGTATTGTGGCA
* * * * * ** *
2668 AAAAA-T-T-AAGAAAAAACTTTTCTGGTAAGTTTTTAGCAAAAATCGTGTAATAACCATCACGG
706 AAAAATTGTAAAGAAATAA--TTTCGGGTCAGTTTTCATCCGAAATCGTGTACTAACCATCACGG
* * **
2730 -TTTTGGCTAAAAACGCGTTCCCGA-GCCCCGACTCAATTTTGCTTGATTTTTTGCGCA-AAA-A
769 TTTTTGGCTAAAAACGCGTT-TCGAGGCCCCGGCTCAATTTTGAATGA-TTTTTG-GCAGAAAGA
* * * *
2791 CTCCTTGAAATATGTATATTCATCAAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTT
831 CTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATATAAGGATTT-TTTTT
* * * * * * * * *
2856 ACGAGCATCTTAATCTTATTTCGATTTACTTAGAAATTAATTAGGAAAAAAATTTGAAAAATG-A
895 ACGAGCATCTAAATATTGTTTCGATTTAATTAGAAATAAATT-CGAAAAAAAATGGAATAA-GCA
**
2920 TATTGGAAGCATGA-
958 TATTTAAAG--TGAG
* ** * * * * * * *
2934 AAAAACC-ATCAATATTTTTGGTGTTAAATTATATATTTTTTCTGAGTATTGTGG-GAAAAAATT
1 AAAAACCTTTCTTTCTTTTTTGCGTTGAATTGTATATTTTTTCTGACTATTGTGGAAAAAAAATT
* * ** *
2997 GTA-AAAAAATAATTTC-G----G---TT-C-AGTTTTTATCCGAAATCGTGTACTAACCATCAC
66 G-AGGAAAAAT-TTTTCGGATAAGTTTTTGCAAAATTTTATCCGAAATCGTTTACT-A--ATCAC
* * * * * * * *
3051 AGTTTTTGGGTT-TAAAACGCGTTTCGGGGCCCCGGATCAATTTTGCATGATTTTTGGCAG-AAA
126 GGTTTAT-GATTAT-AAACGCGTTCCAGGGCCCCGGCTCAATTTTGCAAGATTTTTGAC-GCAAA
* * * *
3114 GACTCCTTGAAATATCT-TTATTCATCT-AACCAAATCTCAGGCACAGTAGACT-TAAGGATTTA
188 GACTCCTTGAAATATCTATT-TTCAT-TGAACCAAATCTCAGCCATATTGGA-TATAAGGATTT-
* * * * * *
3176 TTTTTACGAGCATCTGAATATTGTTTCGATTTAAATAGAAATAAATT-GTAAAAAAATGGAATAA
249 TTTTT-CGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAA
* * ** * * *
3240 CCATATTTA-AAGCGAGAAAA-CCTTTC-AT-TTTTGTATGCGTTGAATTGTGTATTTTTTCTGA
313 CGATA-TTAGAAGCGTGAAAAGCCCATCAATATTTT-T-GGCGTTGAATTATATATTTTTTCTGA
* * * * * * *
3301 CTATTGTGGCAAAAAAACTGAGGAAAAATTTTTCGGATCAGTTTTT-GTAAAATTTTATCCGAAA
375 GTATTGTGAC-AAAAAATTAAGAAAAAACTTTTCGG-TCAGTTTTTAG-CAAA----AT-CG---
* ** * * * *** *
3365 TTGT--TTACTCATCACGGTTTATGATTATAAACGCGTTCCGGGGTTTC-AGCTCAGTTTTGCA-
429 -TGTACTAAC-CATCACGGTTT-TGGCTAAAAACGCGTTCCCGAGCCCCGA-CTCAATTTTGCAT
* * * * * *
3426 AGATTTTAGACGCAAAAACTCCTTGAAATATCTATATTCAT-GAATCAAATCTCAGCAATATTCG
490 A-ATTTTTGGCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGG
* **** * *
3490 ATATAAGGATTTCTTTTTTTTTTTGCATC-GCAATCTTGTTTCGACTTAAATAGAAATTAATTCG
554 ATATAAGGA-TT-TGTTTTTACGAGCATCTG-AATCTTGTTTCGATTTAATTAGAAATTAATTCG
* * * **
3554 GAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG-CCTATCAA-CTTTTTTGGCGTCCAAT
616 GAAAAAAAATGGAAAAATGATATTAGAAGCATGAAAAGACC-ATCAATC-TTTTTGGTGTTGAAT
* * * * * *
3617 TATATACTTTTTCTGAGTATTGTGCCAAAAAGTTG-AGAA-AAA-ACTTTTCGGGTCAATTTTTA
679 TATATATTTTTTCTGAGTATTGTGGCAAAAAATTGTA-AAGAAATA-ATTTCGGGTCAGTTTTCA
* ** * *
3679 GT-CGAAATCGTGTACTAACCATCATGGTTTTTAACTAAAAATGCG-TTC-AGGAGCCCCGACTC
742 -TCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGA-G-GCCCCGGCTC
* * *
3741 AATTTTGCATGGTTTTTGG-AGCAAAGACTCCTTGAAATATCTATTTTCAT-TGAACCAAATCTC
804 AATTTTGAATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCT-AACCAAATCTC
* ** * * * * * *
3804 AGCCATATCGGATATAATGA-TTTTTTTCCGAGCATCTCAATCTTGTTTCAATTTAATTAGGAAT
867 AGCCACATTAGATATAAGGATTTTTTTTACGAGCATCTAAATATTGTTTCGATTTAATTAGAAAT
* * * * * *
3868 TAATTCGGAAAAAAAATGGAAAAACCATA-ATAGAAGCGTG
932 AAATTC-GAAAAAAAATGGAATAAGCATATTTA-AAGTGAG
* ** * * * * * *
3908 AAAAGCCCGTCATTATTTTTGGCGTTGAATTATATATTTTTTTCTGAGTATTGTGG-CAAAAAAT
1 AAAAACCTTTCTTTCTTTTTTGCGTTGAATTGTATA-TTTTTTCTGACTATTGTGGAAAAAAAAT
* * * * * *
3972 TAAGAAAAAACTTTTCTGG-TAAG---TT-C----GTGTA--C-TAA-C-----C--ATCACGGT
65 TGAGGAAAAATTTTTC-GGATAAGTTTTTGCAAAATTTTATCCGAAATCGTTTACTAATCACGGT
* ** * * * * * * * **
4017 TTTTGGCTAAAAATGCATTCC-GAGCCCCGACTCAATTTTGTATGATTTTTGGTGCCAAA-ACTC
129 TTATGATTATAAACGCGTTCCAGGGCCCCGGCTCAATTTTGCAAGATTTTTGACG-CAAAGACTC
* * * * * *
4080 CTTGAAATATGTATATTT-ATCGAACCAAATGTCAGCCACATTGGAAATAAGGTTTTGTTTTTAC
193 CTTGAAATATCTAT-TTTCATTGAACCAAATCTCAGCCATATTGGATATAAGGATTT-TTTTT-C
* * *
4144 GAGCATCTGAATCTTGTTTCGTTTTAATTAGAAATTAATTCGGAAAAAAAATTGGAAAAACGAGA
255 GAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAA-TGGAAAAACGATA
* * * * *
4209 TTAGAAGCATGAAAAGACCATCAATCTTTTTGGTGTTTAATTATATATTTTTTCTGAGTATTGTT
318 TTAGAAGCGTGAAAAGCCCATCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTG-T
* * *
4274 G-CAAAAAATTGTAA-AAAAATA-ATTTCGGGTCAGTTTTTATCCGAAATCGTGTATTAACTAAC
382 GACAAAAAA-T-TAAGAAAAA-ACTTTTC-GGTCAGTTTTTA-GCAAAATCGTG---T-ACTAAC
* * * * * * * * *
4336 CATCACGGTTTTAGGGCTAAAAACGCATTTCGGGGCCCTGGCTCAGTTTTGCATGATTTTTGGTA
438 CATCACGGTTTT--GGCTAAAAACGCGTTCCCGAGCCCCGACTCAATTTTGCATAATTTTTGG-C
* * * * *
4401 G-AAAGACTCCTTGAAATATCTATACTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATT
500 GCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATT
* * * *
4465 TGTTTTTACGAGCATCTGAATATTTGTTTCGATTTAATTAGAAATAAATT-GG-TAAAAAACGGA
565 TGTTTTTACGAGCATCTGAAT-CTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGA
* ** * * * * * * * * * *
4528 ATAACCATATTTA-AAGCAAGAAAA-ACCTTTCATTTTTTTTTGCGTTGAATTGTGTATATTTTA
629 AAAATGATA-TTAGAAGCATGAAAAGACC-ATCAATCTTTTTGGTGTTGAATTATATATTTTTTC
* * * *
4591 TGACTATTGCGGCAAAAAAATTG-AGGAA-AAAT-TTTTCGGATCAGTTTTTACAAATTTTATCC
692 TGAGTATTGTGGC-AAAAAATTGTA--AAGAAATAATTTCGGGTCAG-TTTT-C-------ATCC
* * * ** * * *
4653 GAAATTGTTTACT---CATCACGGTTTATGATTAAAAACGCGTTTCGGGGCCCCAGCTCAGTTTT
745 GAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGAGGCCCCGGCTCAATTTT
* * * * * * *
4715 GCAA-GATTTTTGAC-GTAAAGACTCCTTAAAATATCTATATCCATCGAATCAAATCTCAGCAAT
810 G-AATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCAC
* *** * * * * *
4778 ATTGGATATAAGGATTTCTTTTTTTTAGCATCTCAATCTTGTTTCGACTTAAATAGAAATTAATT
873 ATTAGATATAAGGATTT-TTTTTACGAGCATCTAAATATTGTTTCGATTTAATTAGAAATAAATT
* * *
4843 CGAAAAAAAAAGGAA-AAACGATATTAGAAAAGT--G
937 CGAAAAAAAATGGAATAAGC-ATATT--TAAAGTGAG
** * ** * * * *
4877 AAAATGCTATCAATC-TTTTTGACGTCT-AATTATATACTTTTTCTGAGTATTGTGGCAAAAAAA
1 AAAAACCTTTCTTTCTTTTTTG-CGT-TGAATTGTATATTTTTTCTGACTATTGTGGAAAAAAAA
* * * * * *
4940 TTGA-GAGAAACTTTTCGGTTCAGTTTTT-----A----GT-CGAAATC----A-T-GT-A---T
64 TTGAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTTTATCCGAAATCGTTTACTAATCACGGT
** * * * * * *
4984 TT-TGGCTAAAAACGCGTT-CAGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGGAAAGACTG
129 TTATGATTATAAACGCGTTCCAGG-GCCCCGGCTCAATTTTGCAAGATTTTTGACGCAAAGACTC
*
5047 CTTGAAATATCTATTTTCATTGAACCAAATCTCAGCCATATTGGATATGAGGATTTTTTTTTTCG
193 CTTGAAATATCTATTTTCATTGAACCAAATCTCAGCCATATTGGATATAAGGA--TTTTTTTTCG
* * *
5112 AGCATCTCAATCTTGTTTTGATTTAATTAGGAATTAATTTGGAAAAAAATGGAAAAACGATATTA
256 AGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTA
* * * *
5177 GAAGCGTGAAATGCCCGTCAATCTTTTTAGCGTTGAATTATATATTTTGTTCTGAGTATTGTGGA
321 GAAGCGTGAAAAGCCCATCAATATTTTTGGCGTTGAATTATATATTTT-TTCTGAGTATTGT-GA
* *
5242 AAAAAAATTAAGAAAAAACTTTTCTGGTCAGTTTTTAGTCAAAATCGTGTATTAACCATCACGGT
384 CAAAAAATTAAGAAAAAACTTTTC-GGTCAGTTTTTAG-CAAAATCGTGTACTAACCATCACGGT
* * * * *
5307 TTTTGCTAAAAACGCGTTCCCGAG-CCCTAGCTCAATTTTGCATGATTTTTGGCGCAAAACCTTC
447 TTTGGCTAAAAACGCGTTCCCGAGCCCCGA-CTCAATTTTGCATAATTTTTGGCGCAAAAACTCC
*
5371 TTGAAATATCTATATTCATCGAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTACGA
511 TTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGA
* *
5436 GCATCTGAATCTTGTTTCGATTGAATTAGAAATTAATTCGGAAAAAAATTGGAAAAATGATATTA
576 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAATGATATTA
5501 GAAGCATGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTT-TCGAGTATTGTGGC
641 GAAGCATGAAAAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTCT-GAGTATTGTGGC
* * * * * *
5565 AAAAAATTCTAAAAAAAAAGGATTTCGGGTCAGTTTTTATCCGAAATCTTGTACTAACCATAACG
705 AAAAAATTGTAAAGAAATA--ATTTCGGGTCAGTTTTCATCCGAAATCGTGTACTAACCATCACG
* * *
5630 ATTTTTGGGCTAAAAACGCGTTTCGAGGCCCCGGCTCAATTTTGTATTATTTTTGGCAGAAAGAC
768 GTTTTT-GGCTAAAAACGCGTTTCGAGGCCCCGGCTCAATTTTGAATGATTTTTGGCAGAAAGAC
* *
5695 TCCTTGAAATATCTATATTCATCTAACCAAGTCTCAGCCACATTAGATTTAAGGATATTTTTTTA
832 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATATAAGGAT-TTTTTTTA
* * * * * *
5760 CAAGCATTTGAATATTGTTTCGATTTAATTAGAAATAAATT-G-GAAAAACTGGAATAACCATAT
896 CGAGCATCTAAATATTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGAATAAGCATAT
*
5823 TTAAAGCGAG
961 TTAAAGTGAG
* * *
5833 AAAAACCTTTCTTT-TTTTTTGCGTTGAATTGTGTATTTTTTTCTAACTGTTGTGGCAAAAAAAA
1 AAAAACCTTTCTTTCTTTTTTGCGTTGAATTGTATA-TTTTTTCTGACTATTGTGG-AAAAAAAA
* * * *
5897 TTGA-GAAAATATTTTTCGGATCAGTTTTTGCAAAATTTTATCCGAAATCGTTTAGTTATCACGA
64 TTGAGGAAAA-ATTTTTCGGATAAGTTTTTGCAAAATTTTATCCGAAATCGTTTACTAATCACGG
* *
5961 TTTATGATTAAAAACGCGTTCC-GTGGCCCCGGCTCAATTTTGCAAGATTTTTGACGTAAAGACT
128 TTTATGATTATAAACGCGTTCCAG-GGCCCCGGCTCAATTTTGCAAGATTTTTGACGCAAAGACT
* * * ** * * *
6025 TCTTGAAATATCTATATTCATCGAATTAAATCTTAGCAATATTGGATATAAGGATTTCTTTTTTT
192 CCTTGAAATATCTATTTTCATTGAACCAAATCTCAGCCATATTGGATATAAGGA-TT-TTTTTTC
* * * * *
6090 GAGCATCTCAATCTTATTTCAACTTAAATAGAAATTAATTCGG-TAAAAATGGAAAAACGATATT
255 GAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATT
* * * * * * * *
6154 AAAAGCGTGAAAAGCCTATCAATCTTTTTTGCATTTAATTATATACTTTTTCTGAGTATTGTGGC
320 AGAAGCGTGAAAAGCCCATCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGAC
* * * * *
6219 AAAAAATTGAGAAAAAAACTTTTCGGATCAGTTTTTAGTCGAAATCATGTACTAATCATCACGAT
385 AAAAAATTAAG-AAAAAACTTTTCGG-TCAGTTTTTAG-CAAAATCGTGTACTAACCATCACG-G
*
6284 TTTTCGCTAAAAACGC
446 TTTTGGCTAAAAACGC
6300 ATTTGACTAA
Statistics
Matches: 4470, Mismatches: 618, Indels: 465
0.80 0.11 0.08
Matches are distributed among these distances:
954 19 0.00
955 10 0.00
956 45 0.01
957 32 0.01
958 148 0.03
959 33 0.01
960 132 0.03
961 239 0.05
962 93 0.02
963 134 0.03
964 56 0.01
965 111 0.02
966 142 0.03
967 187 0.04
968 154 0.03
969 79 0.02
970 168 0.04
971 24 0.01
972 2 0.00
973 117 0.03
974 150 0.03
975 349 0.08
976 229 0.05
977 1035 0.23
978 119 0.03
979 399 0.09
980 264 0.06
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (970 bp):
AAAAACCTTTCTTTCTTTTTTGCGTTGAATTGTATATTTTTTCTGACTATTGTGGAAAAAAAATT
GAGGAAAAATTTTTCGGATAAGTTTTTGCAAAATTTTATCCGAAATCGTTTACTAATCACGGTTT
ATGATTATAAACGCGTTCCAGGGCCCCGGCTCAATTTTGCAAGATTTTTGACGCAAAGACTCCTT
GAAATATCTATTTTCATTGAACCAAATCTCAGCCATATTGGATATAAGGATTTTTTTTCGAGCAT
CTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGC
GTGAAAAGCCCATCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGACAAAAAA
TTAAGAAAAAACTTTTCGGTCAGTTTTTAGCAAAATCGTGTACTAACCATCACGGTTTTGGCTAA
AAACGCGTTCCCGAGCCCCGACTCAATTTTGCATAATTTTTGGCGCAAAAACTCCTTGAAATATC
TATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAAT
CTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAATGATATTAGAAGCATGAA
AAGACCATCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGTA
AAGAAATAATTTCGGGTCAGTTTTCATCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAA
AACGCGTTTCGAGGCCCCGGCTCAATTTTGAATGATTTTTGGCAGAAAGACTCCTTGAAATATCT
ATATTCATCTAACCAAATCTCAGCCACATTAGATATAAGGATTTTTTTTACGAGCATCTAAATAT
TGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGAATAAGCATATTTAAAGTGAG
Found at i:3047 original size:323 final size:320
Alignment explanation
Indices: 100--6299 Score: 4882
Period size: 329 Copynumber: 19.1 Consensus size: 320
90 TTTTGCAAAA
* ** * * * *
100 TTTTATCCGAAATCGTTTACT-A--ATCACGGTTTATGATTATAAACGCGTTCCAG-GTTCCCGG
1 TTTTATCCGAAATCGTGTACTAACCATCACGGTTT-TGGCTAAAAACGCGTTCCCGAG-CCCCGA
* * * * * *
161 CTCAGTTTTGCAAGATTTTTGACGCAAAGACTCCTTGAAATATCTATTTTTATTGAACCAAATCT
64 CTCAATTTTGCATGATTTTTG-CGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * * * *
226 CAGCCATATCGGATATAAGGA--TGTTTTTTCGAGCATATCAATCTTGTTTCGATTTAATTAGGA
128 CAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAA
* * * * * * *
289 ATTAATTCGGAAAAAAAAATGGAAAAAACCATAATAGAAGCGTGAAAAGCCCGTAAATATTTTTG
193 ATTAATTCGG--AAAAAAATGG-AAAAACGATATTAGAAGCATGAAAAGACCATCAATCTTTTTG
* *
354 GCGTTGAATTATATATTTTTTCTGAGTTTTGTGTCAAAAAA-T-TAAGAAAAA-ACTTTTCTGGT
255 GCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGTAA-AAAAATA-TTTTC-GGT
*
416 AAGT
317 CAGT
* * * *
420 TTTTA-GCAAATATCGTGTACTAACCATCACTGCTTTTGGCTAAAAACGCGTTCCCGAGCCCCGG
1 TTTTATCCGAA-ATCGTGTACTAACCATCAC-GGTTTTGGCTAAAAACGCGTTCCCGAGCCCCGA
* * * * *
484 CTCAATTTTGCATAATTTTTGGCGCAAAAACTCCTTGAAATATGTATATTTATTGAACCAAATGT
64 CTCAATTTTGCATGATTTTT-GCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * * * *
549 CAGCCACACTGGATATAAGGATATGTTTTTACGAGCATCTGAATCCTGTTTCGTTTTAATTAGAA
128 CAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAA
*
614 ATTAATTCGGAAAAAAATTTGGAAAAATGATATTAGAAGCATGAAAAGACCATCAATCTTTTTGG
193 ATTAATTCGGAAAAAAA--TGGAAAAACGATATTAGAAGCATGAAAAGACCATCAATCTTTTTGG
* * * *
679 TGTTGAATTATATATTTTTTCTGAGTATTATGGCAAAAAATTGTAAAGAAATAATTTCGGGTCAG
256 CGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGTAAAAAAATATTTTC-GGTCAG
744 T
320 T
* * * * *
745 TTTCATCCGAAATCGTGTACTAATCATCACGGTTTTTTGGTTAAAAAACGCATT-TCGAGGCCCC
1 TTTTATCCGAAATCGTGTACTAACCATCACGG--TTTTGGCT-AAAAACGCGTTCCCGA-GCCCC
* * ** * * * *
809 GGCTCAGTTTTAAATGAATTTTG-GCAGGGAGACTCCTTGAAATATCTATATTCATCTAACCAAA
62 GACTCAATTTTGCATGATTTTTGCGCA--AAAACTCCTTGAAATATCTATATTCATCGAACCAAA
* * * * *
873 TCTCGGCCACATTAGATTTAAGGATTT-TTTTTACGAGCATCTAAATATTGTTTCGATTTAATTA
125 TCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTA
* * * * * **
937 GAAATAAATT-GTAAAAAAATGGAATAA-GCATATTTA-AAG--TGAGAAAAACCTTTCTTTTCT
190 GAAATTAATTCGGAAAAAAATGGAAAAACG-ATA-TTAGAAGCATGA-AAAGACC-ATC-AATCT
* * * * * *
997 TTTTTGCGTTGAATTGTCTATTTTTTCTGACTATTGTGGTAAAAAAAATTG-AGGAAAAAT-TTT
250 TTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGG--CAAAAAATTGTA-AAAAAATATTT
*
1060 TCGGATAAGTTTTT
312 TCGG-TCAG----T
* ** * * *
1074 GCAAAATTTTATCCGAAATCGTTTACT-A--ATCACGGTTTATGATTATAAACGCGTTCCAGGGC
1 ------TTTTATCCGAAATCGTGTACTAACCATCACGGTTT-TGGCTAAAAACGCGTTCCCGAGC
* * * * * *
1136 CCCGGCTCAGTTTTGCAAGATTTTTGACGCAAAGACTCCTTGAAATATCTATTTTCATTGAACCA
59 CCCGACTCAATTTTGCATGATTTTTG-CGCAAAAACTCCTTGAAATATCTATATTCATCGAACCA
* * *
1201 AATCTCAGCCATATCGGATATAAGGATTT-TTTTT-CGAGCATATCAATCTTGTTTCGATTTAAT
123 AATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAAT
* * * * * * *
1264 TAGGAATTAATTCGGAAAAAAATGGAAAAACCATAATAGAAGCGTGAAAAGCCCGTCAATATTTT
188 TAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCATGAAAAGACCATCAATCTTTT
* *
1329 TGGCGTTGAATTATATATTTTTTCTAAGTATTGTGACAAAAAA-T-TAAGAAAAA-ACTTTTCTG
253 TGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGTAA-AAAAATA-TTTTC-G
*
1391 GTAAGT
315 GTCAGT
* ** * * * *
1397 TTTTAGCAAAAACCGTGTACTAATCATCTCTGCTTTTGGCTAAAAACGCGTTCCCGAGCCCCGAC
1 TTTTATCCGAAATCGTGTACTAACCATCAC-GGTTTTGGCTAAAAACGCGTTCCCGAGCCCCGAC
* * * * *
1462 TCAATTTTGCATAATTTTTGGCGCAAAAACTCCTTGAAATATGTACATTTATCGAACCAAATTTC
65 TCAATTTTGCATGATTTTT-GCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTC
* * * * * * * *
1527 AACCAAACTGGAAATAAGGTTTTGTTTTTACGAGCATCTGAATCCTGTTTCGTTTTAATTAGAAA
129 AGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAA
**** * *
1592 TTAATTCGGAAATTTTTTTTGGAAAAATGAT-TTAGAAGCATGAAAAGACCATCAATCTTTTTGT
194 TTAATTCGGAAA---AAAATGGAAAAACGATATTAGAAGCATGAAAAGACCATCAATCTTTTTGG
* * * *
1656 TGTTGAATTATATATTTTTTCTGAGTATTATGGCAAAAAATTGTAAAGAAATAATTTCGGGTCAG
256 CGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGTAAAAAAATATTTTC-GGTCAG
1721 T
320 T
* * * * *
1722 TTTCATCCGAAATTGTGTACTAATCATCACGGTTTTTTGGCTAAAAAACGCATT-TCGAGGCCCC
1 TTTTATCCGAAATCGTGTACTAACCATCACGG--TTTTGGCT-AAAAACGCGTTCCCGA-GCCCC
* * ** * * *
1786 GGCTCAGTTTTAAATGATTTTTG-GCAGGGAGACTCCTTGAAATATCTATATTCATCTAACCAAA
62 GACTCAATTTTGCATGATTTTTGCGCA--AAAACTCCTTGAAATATCTATATTCATCGAACCAAA
* * * * * *
1850 TCTCGGCCACCTTAGATTTAAGGATTT-TTTTTACGAGCATCTAAATATTGTTTCGATTTAATTA
125 TCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTA
* * * * ** * *
1914 GAAATAAATT-GTAAAAAAATGGAATAA-GCATATTTA-AAG--TGAGAAAAAGCTTTC-TTTTT
190 GAAATTAATTCGGAAAAAAATGGAAAAACG-ATA-TTAGAAGCATGA-AAAGA-CCATCAATCTT
* * * * * * *
1973 TTTTGCATTGAATTGTCTATTTTTTCTGACTATTGTGGTAAAAAAAATTG-AGGAAAAAT-TTTT
251 TTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGG--CAAAAAATTGTA-AAAAAATATTTT
*
2036 CGGATAAGTTTTT
313 CGG-TCAG----T
* ** * *
2049 GCAAAATTTTATCCGAAATCGTTTACT---CATCACGGTTTATGATTATAAACGCGTTCCAGAGC
1 ------TTTTATCCGAAATCGTGTACTAACCATCACGGTTT-TGGCTAAAAACGCGTTCCCGAGC
* * * * * * *
2111 CCCGGCTTAGTTTTGCAAGATTTTTGACGTAAAGACTCCTTGAAATATCTATATTCATCGAATCA
59 CCCGACTCAATTTTGCATGATTTTTG-CGCAAAAACTCCTTGAAATATCTATATTCATCGAACCA
* * * * * ** * *
2176 AATCTCAGCAATATAGGATATAAGAATTTCTTTTTTTGAGCATCTCAATCTTGTTTCGACTTAAA
123 AATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAAT
* *
2241 TAGAAATTAATTCGGAAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG-CATATCAAAT-
188 TAGAAATTAATTCGG--AAAAAAATGGAAAAACGATATTAGAAGCATGAAAAGAC-CATC-AATC
** * * * *
2304 TTTTTGGCGTCCAATTATATACTTTTTCTGAGTATTGTGCCAAAAAGTTG-AGAAAAAA-CTTTT
249 TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGTA-AAAAAATATTTT
2367 CGAGTCAGT
313 CG-GTCAGT
** * **
2376 TTTTAGT-CGAAATCGTGTACTAACCATCACGGTTTTTAACTAAAAATGCGTTCAGGAGCCCCGA
1 TTTTA-TCCGAAATCGTGTACTAACCATCACGG-TTTTGGCTAAAAACGCGTTCCCGAGCCCCGA
* * *
2440 CTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATTTTCATTGAACCAAATCT
64 CTCAATTTTGCATGATTTTT-GCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * * * * *
2505 CAGCCATATCGGATATAATGA-TT-TTTTTCCGAGCGTCTCAATCTTGTTTCGATTTAATTAGGA
128 CAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAA
* * * * * *
2568 ATTAATTCGGAAAAAAAATGGAAAAACCATAATAGAAGCGTGAAAAGCCCGTCAATATTTTTGGC
193 ATTAATTCGG-AAAAAAATGGAAAAACGATATTAGAAGCATGAAAAGACCATCAATCTTTTTGGC
*
2633 GTTGAATTATATATTTTTTTCTGAGTATTGTGGCAAAAAA-T-TAAGAAAAA-ACTTTTCTGGTA
257 GTTGAATTATATA-TTTTTTCTGAGTATTGTGGCAAAAAATTGTAA-AAAAATA-TTTTC-GGTC
2695 AGT
318 AGT
* ** *
2698 TTTTAGCAAAAATCGTGTAATAACCATCACGGTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACT
1 TTTTATCCGAAATCGTGTACTAACCATCACGGTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACT
* * * *
2763 CAATTTTGCTTGATTTTTTGCGCAAAAACTCCTTGAAATATGTATATTCATCAAACCAAATGTCA
66 CAATTTTGCATGA-TTTTTGCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCA
* * *
2828 GCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTTAATCTTATTTCGATTTACTTAGAAAT
130 GCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAAT
* * * * * * *
2893 TAATTAGGAAAAAAATTTGAAAAATGATATTGGAAGCATGAAAAAACCATCAATATTTTTGGTGT
195 TAATTCGGAAAAAAA-TGGAAAAACGATATTAGAAGCATGAAAAGACCATCAATCTTTTTGGCGT
* * *
2958 TAAATTATATATTTTTTCTGAGTATTGTGGGAAAAAATTGTAAAAAAATAATTTCGGTTCAGT
259 TGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGTAAAAAAATATTTTCGG-TCAGT
* * * * * *
3021 TTTTATCCGAAATCGTGTACTAACCATCACAGTTTTTGGGTTTAAAACGCGTTTCGGGGCCCCGG
1 TTTTATCCGAAATCGTGTACTAACCATCAC-GGTTTT-GGCTAAAAACGCGTTCCCGAGCCCC-G
* *
3086 A-TCAATTTTGCATGATTTTTG-GCAGAAAGACTCCTTGAAATATCTTTATTCATCTAACCAAAT
63 ACTCAATTTTGCATGATTTTTGCGCA-AAA-ACTCCTTGAAATATCTATATTCATCGAACCAAAT
* * * * * * *
3149 CTCAGGCACAGTAGACT-TAAGGATTTATTTTTACGAGCATCTGAATATTGTTTCGATTTAAATA
126 CTCAGCCACATTGGA-TATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTA
* * * * *
3213 GAAATAAATT-GTAAAAAAATGGAATAACCATATTTA-AAGC--GAGAAA-ACCTTTC-AT-TTT
190 GAAATTAATTCGGAAAAAAATGGAAAAACGATA-TTAGAAGCATGA-AAAGACC-ATCAATCTTT
* * * * * *
3271 TGTATGCGTTGAATTGTGTATTTTTTCTGACTATTGTGGCAAAAAAACTG-AGGAAAAAT-TTTT
252 T-T-GGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAAATTGTA-AAAAAATATTTT
3334 CGGATCAGTTTTTGT
313 CGG-TCA------GT
* * ** * * * ***
3349 AAAATTTTATCCGAAATTGTTTACT---CATCACGGTTTATGATTATAAACGCGTTCCGGGGTTT
1 ----TTTTATCCGAAATCGTGTACTAACCATCACGGTTT-TGGCTAAAAACGCGTTCCCGAGCCC
* * * *
3411 C-AGCTCAGTTTTGCAAGATTTTAGACGCAAAAACTCCTTGAAATATCTATATTCAT-GAATCAA
61 CGA-CTCAATTTTGCATGATTTTTG-CGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAA
* * * * **** * *
3474 ATCTCAGCAATATTCGATATAAGGATTTCTTTTTTTTTTTGCATCGCAATCTTGTTTCGACTTAA
124 ATCTCAGCCACATTGGATATAAGGA-TT-TGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAA
* *
3539 ATAGAAATTAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG-CCTATCAA-CT
187 TTAGAAATTAATTCGG-AAAAAAATGGAAAAACGATATTAGAAGCATGAAAAGACC-ATCAATC-
** * * * *
3602 TTTTTGGCGTCCAATTATATACTTTTTCTGAGTATTGTGCCAAAAAGTTG-AGAAAAAA-CTTTT
249 TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGTA-AAAAAATATTTT
*
3665 CGGGTCAAT
313 C-GGTCAGT
* ** * **
3674 TTTTAGT-CGAAATCGTGTACTAACCATCATGGTTTTTAACTAAAAATGCGTTCAGGAGCCCCGA
1 TTTTA-TCCGAAATCGTGTACTAACCATCACGG-TTTTGGCTAAAAACGCGTTCCCGAGCCCCGA
* * * * *
3738 CTCAATTTTGCATGGTTTTTGGAGCAAAGACTCCTTGAAATATCTATTTTCATTGAACCAAATCT
64 CTCAATTTTGCATGATTTTT-GCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * * * * *
3803 CAGCCATATCGGATATAATGA-TT-TTTTTCCGAGCATCTCAATCTTGTTTCAATTTAATTAGGA
128 CAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAA
* * * * * * *
3866 ATTAATTCGGAAAAAAAATGGAAAAACCATAATAGAAGCGTGAAAAGCCCGTCATTATTTTTGGC
193 ATTAATTCGG-AAAAAAATGGAAAAACGATATTAGAAGCATGAAAAGACCATCAATCTTTTTGGC
3931 GTTGAATTATATATTTTTTTCTGAGTATTGTGGCAAAAAA-T-TAAGAAAAA-ACTTTTCTGGT-
257 GTTGAATTATATA-TTTTTTCTGAGTATTGTGGCAAAAAATTGTAA-AAAAATA-TTTTC-GGTC
3992 A--
318 AGT
* * *
3993 ----A---G--TTCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCATT-CCGAGCCCCGAC
1 TTTTATCCGAAATCGTGTACTAACCATCACGG-TTTTGGCTAAAAACGCGTTCCCGAGCCCCGAC
* * * * * *
4048 TCAATTTTGTATGATTTTTGGTGCCAAAACTCCTTGAAATATGTATATTTATCGAACCAAATGTC
65 TCAATTTTGCATGATTTTT-GCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTC
* * * *
4113 AGCCACATTGGAAATAAGGTTTTGTTTTTACGAGCATCTGAATCTTGTTTCGTTTTAATTAGAAA
129 AGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAA
* *
4178 TTAATTCGGAAAAAAAATTGGAAAAACGAGATTAGAAGCATGAAAAGACCATCAATCTTTTTGGT
194 TTAATTCGG-AAAAAAA-TGGAAAAACGATATTAGAAGCATGAAAAGACCATCAATCTTTTTGGC
* * *
4243 GTTTAATTATATATTTTTTCTGAGTATTGTTGCAAAAAATTGTAAAAAAATAATTTCGGGTCAGT
257 GTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGTAAAAAAATATTTTC-GGTCAGT
* * * *
4308 TTTTATCCGAAATCGTGTATTAACTAACCATCACGGTTTTAGGGCTAAAAACGCATTTCGGGGCC
1 TTTTATCCGAAATCGTG---T-ACTAACCATCACGGTTTT--GGCTAAAAACGCGTTCCCGAGCC
* * * * * *
4373 CTGGCTCAGTTTTGCATGATTTTTG-GTAGAAAGACTCCTTGAAATATCTATACTCATCTAACCA
60 CCGACTCAATTTTGCATGATTTTTGCGCA-AAA-ACTCCTTGAAATATCTATATTCATCGAACCA
* * * *
4437 AATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATATTTGTTTCGATTTAA
123 AATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAAT-CTTGTTTCGATTTAA
* * * * * * * * *
4502 TTAGAAATAAATT-GGTAAAAAACGGAATAACCATATTTA-AAGCAAGAAAA-ACCTTTCATTTT
187 TTAGAAATTAATTCGGAAAAAAATGGAAAAACGATA-TTAGAAGCATGAAAAGACC-ATCAATCT
* * * * * * * *
4564 TTTTTGCGTTGAATTGTGTATATTTTATGACTATTGCGGCAAAAAAATTG-AGGAAAAAT-TTTT
250 TTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAAATTGTA-AAAAAATATTTT
4627 CGGATCAGTTTTT
313 CGG-TCAG----T
* * ** * * *
4640 ACAAATTTTATCCGAAATTGTTTACT---CATCACGGTTTATGATTAAAAACGCGTTTCGGGGCC
1 -----TTTTATCCGAAATCGTGTACTAACCATCACGGTTT-TGGCTAAAAACGCGTTCCCGAGCC
* * * * * * *
4702 CC-AGCTCAGTTTTGCAAGATTTTTGACGTAAAGACTCCTTAAAATATCTATATCCATCGAATCA
60 CCGA-CTCAATTTTGCATGATTTTTG-CGCAAAAACTCCTTGAAATATCTATATTCATCGAACCA
* * * *** * *
4766 AATCTCAGCAATATTGGATATAAGGATTTCTTTTTTTTAGCATCTCAATCTTGTTTCGACTTAAA
123 AATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAAT
* * * *
4831 TAGAAATTAATTCGAAAAAAAAAGGAAAAACGATATTAGAA-AAGTGAAAATG-CTATCAATCTT
188 TAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCA-TGAAAA-GACCATCAATCTT
* * * * *
4894 TTTGACGTCT-AATTATATACTTTTTCTGAGTATTGTGGCAAAAAAATTG-AGAGAAA-CTTTTC
251 TTTGGCGT-TGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAAATTGTAAAAAAATATTTTC
4956 GGTTCAGT
314 GG-TCAGT
* **
4964 TTTTAGT-CGAAATC----A-T----GT-A---TTTTGGCTAAAAACGCGTTCAGGAGCCCCGAC
1 TTTTA-TCCGAAATCGTGTACTAACCATCACGGTTTTGGCTAAAAACGCGTTCCCGAGCCCCGAC
* * * * *
5015 TCAATTTTGCATGATTTTTGGCGGAAAGACTGCTTGAAATATCTATTTTCATTGAACCAAATCTC
65 TCAATTTTGCATGATTTTT-GCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTC
* * * * * *
5080 AGCCATATTGGATATGAGGATTTTTTTTTTCGAGCATCTCAATCTTGTTTTGATTTAATTAGGAA
129 AGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAA
* * * * * *
5145 TTAATTTGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAATGCCCGTCAATCTTTTTAGCGT
194 TTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCATGAAAAGACCATCAATCTTTTTGGCGT
* *
5210 TGAATTATATATTTTGTTCTGAGTATTGTGGAAAAAAAAT-TAAGAAAAA-ACTTTTCTGGTCAG
259 TGAATTATATATTTT-TTCTGAGTATTGTGGCAAAAAATTGTAA-AAAAATA-TTTTC-GGTCAG
5273 T
320 T
* * * *
5274 TTTTAGT-CAAAATCGTGTATTAACCATCACGGTTTTTGCTAAAAACGCGTTCCCGAG-CCCTAG
1 TTTTA-TCCGAAATCGTGTACTAACCATCACGGTTTTGGCTAAAAACGCGTTCCCGAGCCCCGA-
* * *
5337 CTCAATTTTGCATGATTTTTGGCGCAAAACCTTCTTGAAATATCTATATTCATCGAACCAAATGT
64 CTCAATTTTGCATGATTTTT-GCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* *
5402 CAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTGAATTAGAA
128 CAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAA
* *
5467 ATTAATTCGGAAAAAAATTGGAAAAATGATATTAGAAGCATGAAAAGACCATCAATCTTTTTGGT
193 ATTAATTCGGAAAAAAA-TGGAAAAACGATATTAGAAGCATGAAAAGACCATCAATCTTTTTGGC
* * *
5532 GTTGAATTATATATTTTTT-TCGAGTATTGTGGCAAAAAATTCTAAAAAAAAAGGATTTCGGGTC
257 GTTGAATTATATATTTTTTCT-GAGTATTGTGGCAAAAAATTGTAAAAAAATA--TTTTC-GGTC
5596 AGT
318 AGT
* * * *
5599 TTTTATCCGAAATCTTGTACTAACCATAACGATTTTTGGGCTAAAAACGCGTT-TCGAGGCCCCG
1 TTTTATCCGAAATCGTGTACTAACCATCACG-GTTTT-GGCTAAAAACGCGTTCCCGA-GCCCCG
* * * * *
5663 GCTCAATTTTGTATTATTTTTG-GCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAGT
63 ACTCAATTTTGCATGATTTTTGCGCA-AAA-ACTCCTTGAAATATCTATATTCATCGAACCAAAT
* * * * * *
5727 CTCAGCCACATTAGATTTAAGGATATT-TTTTTACAAGCATTTGAATATTGTTTCGATTTAATTA
126 CTCAGCCACATTGGATATAAGGAT-TTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTA
* * * * * * *
5791 GAAATAAATT-GG-AAAAACTGGAATAACCATATTTA-AAGCGA-GAAAA-ACCTTTC-TTTTTT
190 GAAATTAATTCGGAAAAAAATGGAAAAACGATA-TTAGAAGC-ATGAAAAGACC-ATCAATCTTT
* * * * * * *
5850 TTTGCGTTGAATTGTGTATTTTTTTCTAACTGTTGTGGCAAAAAAAATTG--AGAAAATATTTTT
252 TTGGCGTTGAATTATATA-TTTTTTCTGAGTATTGTGGC--AAAAAATTGTAAAAAAATA-TTTT
5913 CGGATCAGTTTTT
313 CGG-TCAG----T
*** * ** *
5926 GCAAAATTTTATCCGAAATCGT-T--TAGTTATCACGATTTATGATTAAAAACGCGTT-CCGTGG
1 ------TTTTATCCGAAATCGTGTACTAACCATCACGGTTT-TGGCTAAAAACGCGTTCCCG-AG
* * * * * **
5987 CCCCGGCTCAATTTTGCAAGATTTTTGACGTAAAGACTTCTTGAAATATCTATATTCATCGAATT
58 CCCCGACTCAATTTTGCATGATTTTTG-CGCAAAAACTCCTTGAAATATCTATATTCATCGAACC
* * * * ** * * *
6052 AAATCTTAGCAATATTGGATATAAGGATTTCTTTTTTTGAGCATCTCAATCTTATTTCAACTTAA
122 AAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAA
* * * *
6117 ATAGAAATTAATTCGG-TAAAAATGGAAAAACGATATTAAAAGCGTGAAAAG-CCTATCAATCTT
187 TTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCATGAAAAGACC-ATCAATCTT
* * * *
6180 TTTTGCATTTAATTATATACTTTTTCTGAGTATTGTGGCAAAAAATTG-AGAAAAAA-ACTTTTC
251 TTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGTA-AAAAAATA-TTTTC
6243 GGATCAGT
314 GG-TCAGT
* * * *
6251 TTTTAGT-CGAAATCATGTACTAATCATCACGATTTTTCGCTAAAAACGC
1 TTTTA-TCCGAAATCGTGTACTAACCATCACG-GTTTTGGCTAAAAACGC
6300 ATTTGACTAA
Statistics
Matches: 4750, Mismatches: 817, Indels: 624
0.77 0.13 0.10
Matches are distributed among these distances:
307 2 0.00
308 204 0.04
309 104 0.02
310 61 0.01
311 80 0.02
312 65 0.01
313 6 0.00
314 2 0.00
315 3 0.00
317 16 0.00
318 1 0.00
319 29 0.01
320 124 0.03
321 326 0.07
322 350 0.07
323 513 0.11
324 508 0.11
325 372 0.08
326 165 0.03
327 339 0.07
328 294 0.06
329 529 0.11
330 311 0.07
331 131 0.03
332 96 0.02
333 75 0.02
334 10 0.00
335 19 0.00
337 15 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (320 bp):
TTTTATCCGAAATCGTGTACTAACCATCACGGTTTTGGCTAAAAACGCGTTCCCGAGCCCCGACT
CAATTTTGCATGATTTTTGCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAG
CCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATT
AATTCGGAAAAAAATGGAAAAACGATATTAGAAGCATGAAAAGACCATCAATCTTTTTGGCGTTG
AATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGTAAAAAAATATTTTCGGTCAGT
Found at i:12927 original size:4 final size:4
Alignment explanation
Indices: 12920--12944 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12910 TATATATATA
12920 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
12945 GGCCATGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:13025 original size:2 final size:2
Alignment explanation
Indices: 13018--13044 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13008 TTGTCTTTAA
13018 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
13045 AAGGAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15364 original size:6 final size:6
Alignment explanation
Indices: 15353--15397 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
15343 CGTTTCCAAT
*
15353 TTTTTG TTTTTG TTTTT- TTCTTTG -TTTTG TTTTCG -TTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TT-TTTG TTTTTG TTTTTG TTTTTG TTTTT
15398 ATTATTCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
5 10 0.30
6 23 0.70
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.82
Consensus pattern (6 bp):
TTTTTG
Found at i:15390 original size:11 final size:11
Alignment explanation
Indices: 15354--15397 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
15344 GTTTCCAATT
15354 TTTTGTTTTTG
1 TTTTGTTTTTG
*
15365 TTTTTTTCTTTG
1 TTTTGTT-TTTG
*
15377 TTTTGTTTTCG
1 TTTTGTTTTTG
15388 TTTTGTTTTT
1 TTTTGTTTTT
15398 ATTATTCATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.00, C:0.05, G:0.14, T:0.82
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:31513 original size:21 final size:21
Alignment explanation
Indices: 31482--31527 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
31472 TCGCCACCAG
* *
31482 CTTTTGTTTGTTTTTTTTCTTT
1 CTTTTGTTTGTTCTTCTTC-TT
31504 CTTTT-TTTGTTCTTCTTCTT
1 CTTTTGTTTGTTCTTCTTCTT
31524 CTTT
1 CTTT
31528 GATTATTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 11 0.50
22 5 0.23
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (21 bp):
CTTTTGTTTGTTCTTCTTCTT
Found at i:36845 original size:30 final size:29
Alignment explanation
Indices: 36772--36850 Score: 70
Period size: 30 Copynumber: 2.7 Consensus size: 29
36762 AATTTGTAAC
* *
36772 TTTTGGATGTTTTG-TCACTTGAACTTCAA
1 TTTTGGACGTTTTGCTC-CCTGAACTTCAA
* ** *
36801 TTTTGGTCAATTTGCTCCCTGAATTCTCAA
1 TTTTGGACGTTTTGCTCCCTGAACT-TCAA
*
36831 TTTTGGACGTTTTGCCCCCT
1 TTTTGGACGTTTTGCTCCCT
36851 CTCAATGTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 3
0.75 0.20 0.06
Matches are distributed among these distances:
29 16 0.42
30 22 0.58
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.46
Consensus pattern (29 bp):
TTTTGGACGTTTTGCTCCCTGAACTTCAA
Found at i:40080 original size:11 final size:11
Alignment explanation
Indices: 40066--40103 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
40056 CTTTGACTAC
*
40066 TCTTTTCTTCT
1 TCTTTTTTTCT
40077 TCTTTTTTTCT
1 TCTTTTTTTCT
*
40088 TCTTTTTTTTT
1 TCTTTTTTTCT
40099 TCTTT
1 TCTTT
40104 GATTTGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TCTTTTTTTCT
Found at i:40087 original size:14 final size:14
Alignment explanation
Indices: 40068--40102 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
40058 TTGACTACTC
40068 TTTTCTTCTTCTTT
1 TTTTCTTCTTCTTT
*
40082 TTTTCTTCTTTTTT
1 TTTTCTTCTTCTTT
40096 TTTTCTT
1 TTTTCTT
40103 TGATTTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTTCTTCTTT
Found at i:43734 original size:5 final size:5
Alignment explanation
Indices: 43724--43750 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
43714 ATAAGATATG
43724 ATGAA ATGAA ATGAA ATGAA ATGAA AT
1 ATGAA ATGAA ATGAA ATGAA ATGAA AT
43751 ATCTGTCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.19, T:0.22
Consensus pattern (5 bp):
ATGAA
Found at i:44807 original size:25 final size:24
Alignment explanation
Indices: 44754--44808 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
44744 AATATATCAG
*
44754 ACAA-AAAAAACTAAAGAAAAGAA
1 ACAAGAAAAAACGAAAGAAAAGAA
*
44777 AAAAGAAAAAACGAAATGCAAAAG-A
1 ACAAGAAAAAACGAAA-G-AAAAGAA
44802 ACAAGAA
1 ACAAGAA
44809 CAAGAGAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 3 0.12
24 10 0.38
25 8 0.31
26 5 0.19
ACGTcount: A:0.75, C:0.09, G:0.13, T:0.04
Consensus pattern (24 bp):
ACAAGAAAAAACGAAAGAAAAGAA
Found at i:45240 original size:2 final size:2
Alignment explanation
Indices: 45233--45265 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
45223 CTATAAACAG
45233 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45266 GGAAATGCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:45256 original size:15 final size:15
Alignment explanation
Indices: 45236--45265 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
45226 TAAACAGATA
45236 TATATATATATATAT
1 TATATATATATATAT
45251 TATATATATATATAT
1 TATATATATATATAT
45266 GGAAATGCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:61040 original size:102 final size:102
Alignment explanation
Indices: 60923--61127 Score: 365
Period size: 102 Copynumber: 2.0 Consensus size: 102
60913 TAAGGATGCC
* *
60923 GCCGGTGCCACCGTATCAGGTTCAACTTCAAGTGATTCCAAAGGCTCTGGCGCCACCTCTGCATC
1 GCCGGCGCCACCGTATCAGGTTCAACTTCAAGTGATTCCAAAGGCTCCGGCGCCACCTCTGCATC
*
60988 AACTTCAAAGGATTCCAAAGGCTCTGGCACCGTATCA
66 AACTTCAAAGGATGCCAAAGGCTCTGGCACCGTATCA
* *
61025 GCCGGCGCCACCGTATCAGGTTCAGCTTCAAGTGATTCCAAAGGCTCCGGCGCCGCCTCTGCATC
1 GCCGGCGCCACCGTATCAGGTTCAACTTCAAGTGATTCCAAAGGCTCCGGCGCCACCTCTGCATC
61090 AACTTCAAAGGATGCCAAAGGCTCTGGCACCGTATCA
66 AACTTCAAAGGATGCCAAAGGCTCTGGCACCGTATCA
61127 G
1 G
61128 GTTCAACTTC
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 98 1.00
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.21
Consensus pattern (102 bp):
GCCGGCGCCACCGTATCAGGTTCAACTTCAAGTGATTCCAAAGGCTCCGGCGCCACCTCTGCATC
AACTTCAAAGGATGCCAAAGGCTCTGGCACCGTATCA
Found at i:61134 original size:42 final size:42
Alignment explanation
Indices: 61033--61159 Score: 148
Period size: 42 Copynumber: 3.0 Consensus size: 42
61023 CAGCCGGCGC
* *
61033 CACCGTATCAGGTTCAGCTTCAAGTGATTCCAAAGGCTCCGG
1 CACCGTATCAGGTTCAACTTCAAGTGATTCCAAAGGCTCTGG
* ** * ** *
61075 CGCCGCCTCTGCATCAACTTCAAAG-GATGCCAAAGGCTCTGG
1 CACCGTATCAGGTTCAACTTC-AAGTGATTCCAAAGGCTCTGG
*
61117 CACCGTATCAGGTTCAACTTCAAGTGATTCCAAAGCCTCTGG
1 CACCGTATCAGGTTCAACTTCAAGTGATTCCAAAGGCTCTGG
61159 C
1 C
61160 TCTGGCTCTG
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
41 3 0.05
42 60 0.91
43 3 0.05
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.23
Consensus pattern (42 bp):
CACCGTATCAGGTTCAACTTCAAGTGATTCCAAAGGCTCTGG
Found at i:62574 original size:22 final size:22
Alignment explanation
Indices: 62546--62597 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
62536 AGTGTTGTTA
*
62546 AGGCGCTCGCCTACGCGCGTCT
1 AGGCGCTCGCCTACGCGCGCCT
*
62568 AGGCGCTTGCCTACGCGCGCCT
1 AGGCGCTCGCCTACGCGCGCCT
62590 AGGCGCTC
1 AGGCGCTC
62598 AGGTGAGGCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.10, C:0.40, G:0.33, T:0.17
Consensus pattern (22 bp):
AGGCGCTCGCCTACGCGCGCCT
Found at i:63021 original size:12 final size:12
Alignment explanation
Indices: 63004--63028 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62994 AAAGTCAACA
63004 GACCTAATTAAC
1 GACCTAATTAAC
63016 GACCTAATTAAC
1 GACCTAATTAAC
63028 G
1 G
63029 GAGACGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (12 bp):
GACCTAATTAAC
Found at i:67646 original size:83 final size:83
Alignment explanation
Indices: 67507--67671 Score: 321
Period size: 83 Copynumber: 2.0 Consensus size: 83
67497 TTCTGTGTGA
67507 GTTGAATATGTCCATGCTAACCACACCAAAGTTTTGGTGAAAATTTTTCTAGCTTGGAGTAATAT
1 GTTGAATATGTCCATGCTAACCACACCAAAGTTTTGGTGAAAATTTTTCTAGCTTGGAGTAATAT
*
67572 CATTTTGAATTAAAAAAT
66 CATTTTGAATAAAAAAAT
67590 GTTGAATATGTCCATGCTAACCACACCAAAGTTTTGGTGAAAATTTTTCTAGCTTGGAGTAATAT
1 GTTGAATATGTCCATGCTAACCACACCAAAGTTTTGGTGAAAATTTTTCTAGCTTGGAGTAATAT
67655 CATTTTGAATAAAAAAA
66 CATTTTGAATAAAAAAA
67672 GGCCAGATAA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (83 bp):
GTTGAATATGTCCATGCTAACCACACCAAAGTTTTGGTGAAAATTTTTCTAGCTTGGAGTAATAT
CATTTTGAATAAAAAAAT
Done.