Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019529.1 Corchorus olitorius cultivar O-4 contig19562, 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: 7280
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1871 original size:956 final size:952
Alignment explanation
Indices: 539--7112 Score: 6183
Period size: 956 Copynumber: 6.8 Consensus size: 952
529 TTGGCAAAAT
** * * * * * *
539 GACTCCTTGAAATATCTATATTTA-TGTAACCAAATCTCAGCCACAATGGATAT-AGGATTTCTT
1 GACTCCTTGAACCATCTATATTCATTG-AAACAAATCTCAGCCATATTGGATATAAAGATTT-GT
* ** * * *
602 TTTACGAGCATCTGAATCTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGAT
64 TTTACGAGCATCTGAATCTTCTTTCGTTTTTCTTAGAAATTAATTCGAAAAAAA-GAAAAACAAT
* *
667 ATTAGAAGCGTGAAAAG-TCCTTCAATTTTTTTTTGGCT-TTGAATTATATATTTTTTCTTAGTA
128 ATTAGAAGCGTGAAAAGCT-CGTCAA--TCTTTTTGG-TGTTGAATTATATA-TTTTTCTTAGTA
* * * * *
730 TTGT-GGAAAAAGATTGAGGATAAAATTTTCAAATCTGCTTTTTCAAAATTTTAGCTGAAATCGT
188 TTGTGGGAAAAA-ATTAAGGA-AAAAATTT----TC-G---GTTC-AATTTTTAGCCGAAATCGT
* * * *
794 GTACTAACCATCACGATTTTTGAATAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTCCAAGGCG
242 GTACTAACCATCACGATTTTTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGACG
* *
859 CAAAGACTCACTGAACCATCTATATTCATTGAAACATATCTCAGCCATATTGGATATAAAGATTT
307 CAAAGACTC-CTGAACCATCTATATTCATTGTAACAAATCTCAGCCATATTGGATATAAAGATTT
*
924 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTATCTAGAAATTAATTCGTAAAAAAA-AGAAAA
371 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTATCTAGAAATTAATTCGGAAAAAAATAGAAAA
* * * * * *
988 ACAATATGAGAAACTTGAAAAGCCCGTCAATATTTTTGGTGTTGAGTAATATATTTTTCTTAGTA
436 ACAATATTAGAAGCTTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTCTTAGTA
1053 TTGTGGC-AAAAATT-AAGAAAAAATTTTCGGTCCAATTTTTAGCCGAAATCGTGTACTAACCAT
501 TTGTGGCAAAAAATTGAAGAAAAAATTTTCGGTCCAATTTTTAGCCGAAATCGTGTACTAACCAT
*
1116 CACGATTTTTGGGCTAAAAACACGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAA
566 CACGATTTTT-GGCTAAAAACGCGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAA
* * * *
1181 AGAATCTTTGAAATATCTATATTTATGTAACAAAATATCAGCCCCAATGGATTTAAGAATTGCTT
630 AGACTCCTTGAAATATCTATATTTATGTAAC-AAATCTCAGCCACAATGGATTTAAGAATTGCTT
1246 TTTACGAGCATCTGAATCTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGAT
694 TTTACGAGCATCTGAATCTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGAT
* *
1311 ATTAGAAGCGTGAAAAATCCTTCAATTTTTTATGGCGTTGAATTATATATTTTTTCATAATATTG
759 ATTAGAAGCGTGAAAAATCCTTCAATTTTTT-TGGCGTTGAATTATATATTTTTTCTTAGTATTG
* * * *
1376 TGGAAAACGATTGAGGATAAACTTTTCAAATCAGCTTTTTCAAAAGTTTAACGGAAATCGTGCAC
823 TGGAAAAAGATTGAGGATAAACTTTTCAAATCAGCTTTTTCAAAAGTTTAGCCGAAATCGTGTAC
* *
1441 TAACCATCACAGTTTTTGACTAAATTTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAA
888 TAACCATCACGGTTTTTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAA
* *
1506 GACTCCTTTAACCATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAAATTTGTTT
1 GACTCCTTGAACCATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTGTTT
*
1571 TACGAGCATCTGAATCTTGTTTCGTTTTTCTTAGAAATTAATTCAGAAAAAATAGAAAAACAATA
66 TACGAGCATCTGAATCTTCTTTCGTTTTTCTTAGAAATTAATTC-GAAAAAA-AGAAAAACAATA
* * * *
1636 TTAGAAGCTTGAAAAGCTCGTCAATATTTTTGGTGTTGAATAACATATTTTTCTTAGTATTGTGG
129 TTAGAAGCGTGAAAAGCTCGTCAATCTTTTTGGTGTTGAATTATATATTTTTCTTAGTATTGTGG
** * * * *
1701 CGAAAAAATTAAGGAAAATTTTTTTGGTTCAATTTATAGCTGAAATCGTGTACTAACCATCACGG
194 -GAAAAAATTAAGGAAAAAATTTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGA
1766 TTTTTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGACGCAAAGACTCACTGAAC
258 TTTTTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGACGCAAAGACTC-CTGAAC
* * *
1831 CATCTATATTCATTGGAACAAATCTCAACCATATTGGATATTAAGATTTGTTTTTACGAGCATCT
322 CATCTATATTCATTGTAACAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGAGCATCT
* *
1896 GAATCTTTTTTCGATTTATCTAGAAATTAATTTGGAAAAAAATAGAAAAACAATATTAGAAGCTT
387 GAATCTTGTTTCGATTTATCTAGAAATTAATTCGGAAAAAAATAGAAAAACAATATTAGAAGCTT
* * *
1961 GAAAAGCGCGTCAATCTTTTTGGCGTTGAATTACATATTTTTCTTAGTATTGTGGCAAAAAAAT-
452 GAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTCTTAGTATTGTGGCAAAAAATTG
* * * * *
2025 CAGAAAAAAATTTTCGGTTCAATTTTTAGTCGAAATCGTG---T-A-C-GCACGAGTTTTAGGCT
517 AAG-AAAAAATTTTCGGTCCAATTTTTAGCCGAAATCGTGTACTAACCATCACGA-TTTTTGGCT
* *
2084 AAAAACACGATTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATA
580 AAAAACGCGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATA
*
2149 TCTATATTTATGTAACCAAATCTCAGCCACAATGGATTTAGGAATTGCTTTTTACGAGCATCTGA
645 TCTATATTTATGTAA-CAAATCTCAGCCACAATGGATTTAAGAATTGCTTTTTACGAGCATCTGA
2214 ATCTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAA
709 ATCTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAA
*
2279 AATCCTTCAATTTTTTATGGTGTTGAATTATATATTTTTTCTTAGTATTGTGGAAAAAGATTGAG
774 AATCCTTCAATTTTTT-TGGCGTTGAATTATATATTTTTTCTTAGTATTGTGGAAAAAGATTGAG
* *
2344 GATAAACTTTACAAATCAGCTTTTTCAAAAGTTTAACCGAAATCGTGTACTAACCATCACGGTTT
838 GATAAACTTTTCAAATCAGCTTTTTCAAAAGTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
*
2409 TTGACTAAAATTGCGTTCCGGAGCCCCAGCTCTGTTTTGCATGGCGCAAA
903 TTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAA
2459 GACTCAC-TGAACCATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTGTT
1 GACTC-CTTGAACCATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTG-T
* * *
2523 TTTACGAGCATCTGAATCTTGTTTCGATTTATC-TAGAAATTAATTCGTAAAAAAAATAGAAAAT
64 TTTACGAGCATCTGAATCTTCTTTCG-TTTTTCTTAGAAATTAATTCG---AAAAAA-AGAAAAA
* * * * *
2587 CATTATTAGTAGCATGAAAAGCCCGTCAATCTTTTTGGTGTTGAATAATATATTTTTCTTAGTAT
124 CAATATTAGAAGCGTGAAAAGCTCGTCAATCTTTTTGGTGTTGAATTATATATTTTTCTTAGTAT
* * *
2652 TGTGGCAAAAAATTAAGAAAAAAATTTTCGGTTCAATTTTTAGCGGAAATCGTGTACTAACCATC
189 TGTGGGAAAAAATTAAGGAAAAAATTTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAACCATC
* * ** * * *
2717 ATGATTTTTGGGCTAAAAACGCGATT-CGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAAAA
254 ACGATTTTT-GACTAAAATTGCG-TTCCGGAGCCCCGGCTCTGTTTTGCATGA-----CGC--AA
** * * * * * * *
2781 AGACTCCTTGAAATATCAATATT--TTAGTATCCAAATCTCAGCCACAATGGATTTAAGGATTTC
310 AGACTCC-TGAACCATCTATATTCATT-GTA-ACAAATCTCAGCCATATTGGATATAAAGATTTG
* * * *
2844 TTTTTACGAGCATCTGAATCTTCTTTCGATTTAAAC-AGAAATAAATTC-GAAAAAAAT-GGAAA
372 TTTTTACGAGCATCTGAATCTTGTTTCGATTT-ATCTAGAAATTAATTCGGAAAAAAATAGAAAA
** ** * *
2906 ATGATATTAGAAG-TGTGAAAAATCCTTCAAT-TTTTCTGGCGTTAAATTATATATTTTTTCTTA
436 ACAATATTAGAAGCT-TGAAAAGCCCGTCAATCTTTT-TGGCGTTGAATTATATA-TTTTTCTTA
* * * * *
2969 GTATTGTGG-AAAAAGATTGAGGATAAAATTTTCAAATCAGCTTTTTCAAAATTTTAGCCGAAAT
498 GTATTGTGGCAAAAA-ATTGAAGA-AAAAATTT----TC-G----GTCCAATTTTTAGCCGAAAT
* ** * *
3033 CGTGTACTAACCATCACGATTTTTGACTAAAATTGCG-TTCCGGAGCCCCGGCTCTGTTTTGC--
552 CGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGATT-CGGGGCCCCGGCTCAGTTTTGCAT
** * * * * *
3095 -A----TGGC-GCAAAGACTCAC-TGAACCATCTATATTCATTGAAACATATCTCAGCCATATTG
616 GATTTTTGGCAG-AAAGACTC-CTTGAAATATCTATATTTA-TGTAACAAATCTCAGCCACAATG
* * * *
3153 GATATAAAGATTTG-TTTTTACGAGCATCTGAATCTTGTTTCGATTT-ATATAGAAATTAATTCG
678 GAT-TTAAGAATTGCTTTTTACGAGCATCTGAATCTTCTTTCGATTTAAT-TAGAAATAAATTCG
* * * ** * * * * *
3216 TAAAAAAATAGAAAAACAATATTAGAAGCTTGAAAAGCCCGTCAATGTTTTTGGTGTTGAGTAAT
741 -AAAAAAAT-GGAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGGCGTTGAATTAT
* ** *
3281 ATA-TTTTTCTTAGTATTGTGGCAAAAA-ATT-AAGA-AAA------AAAT----TTCGGTCCAA
804 ATATTTTTTCTTAGTATTGTGG-AAAAAGATTGAGGATAAACTTTTCAAATCAGCTT-TTTCAAA
** * * * * * *** *
3332 TTTTTAGCCAAAATCGTGTATTAACCATCACGATTTTTGGGCAAAAAACACGATT-CGGGGCCCC
867 AGTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT-GACTAAAATTGCG-TTCCGGAGCCCC
** *** **
3396 GGCTAAGTTTTGCATGATTC-TT
930 GGCTCTGTTTTGCATGGCGCAAA
** * * ** * * *
3418 GA---CTTGAAATATCTATATTTA-TGTAACAAAATCTCAGCCCCAATGGAT-TTAAGAATTGCT
1 GACTCCTTGAACCATCTATATTCATTGAAAC-AAATCTCAGCCATATTGGATATAAAGATTTG--
* ** * * *
3478 TTTTACGAGCATCTGAATCTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGA
63 TTTTACGAGCATCTGAATCTTCTTTCGTTTTTCTTAGAAATTAATTCGAAAAAAA-GAAAAACAA
* * *
3543 TATTAGAAGCGTGAAAA-ATCCTTCAATCTTTTATGGCGTTGAATTATATATTTTTTCTTAGTAT
127 TATTAGAAGCGTGAAAAGCT-CGTCAATCTTTT-TGGTGTTGAATTATATA-TTTTTCTTAGTAT
* * * * * ** *
3607 TGT-GGAAAAAGATTGAGGATACACTTTACAAATCAGCTTTTCAAAAGTTTAACCGAAATCGTGT
189 TGTGGGAAAAA-ATTAAGGAAAAAATTT-----TC-G--GTTC-AATTTTTAGCCGAAATCGTGT
* *
3671 ACTAACCATCACGGTTTTTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCA
244 ACTAACCATCACGATTTTTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGACGCA
* * * *
3736 AAGACTCCTTTAACCATCTATATTCATTGGAACAAATCTCAACCATATTGGATATAAAAATTTG-
309 AAGACTCC-TGAACCATCTATATTCATTGTAACAAATCTCAGCCATATTGGATATAAAGATTTGT
*
3800 TTTTACGAGCATCTGAATCTTGTTTCGTTTTATCTAGAAATTAATTCGGAAAAAAATAGAAAAAC
373 TTTTACGAGCATCTGAATCTTGTTTCGATTTATCTAGAAATTAATTCGGAAAAAAATAGAAAAAC
* * * *
3865 AATATTAGAAGCTTGAAAAGCTCGTCAATCTTTTTGGTGTTGAATAACATATTTTTCTTAGTATT
438 AATATTAGAAGCTTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTCTTAGTATT
* *
3930 GTGGCAAAAAATTCAGAA-AAAAAATTTTCGGTTCAATTTTTAGCGGAAATCGTG---------T
503 GTGGCAAAAAATT--GAAGAAAAAATTTTCGGTCCAATTTTTAGCCGAAATCGTGTACTAACCAT
* * * * * *
3985 ---GATTTTTGGGCTAAAAACGCGATTCGTGGTCTCGGCTCAGTTTTGTATGATTGTTGGCAAAA
566 CACGATTTTT-GGCTAAAAACGCGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAA
* * *
4047 AGACTCCTTGAAATATCTATATTTATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTCTT
630 AGACTCCTTGAAATATCTATATTTATGTAA-CAAATCTCAGCCACAATGGATTTAAGAATTGCTT
* * *
4112 TTTACGAGCATTTGAATCTTCTTTCGATTTAAATAGAAATAAATTCGAAAAAAAAGGAAAACGAT
694 TTTACGAGCATCTGAATCTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGAT
4177 ATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTTAGTATTGT
759 ATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTTAGTATTGT
* *
4242 GGAAAAAGATTGAGGATAAACTTTTCAAATCAGC-TTTTCAAAATTTTAGCCGAAATCTTGTACT
824 GGAAAAAGATTGAGGATAAACTTTTCAAATCAGCTTTTTCAAAAGTTTAGCCGAAATCGTGTACT
4306 AACCATCACGGTTTTTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAA
889 AACCATCACGGTTTTTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAA
* *
4370 GACTCAC-TGAACCATCTATA-TCAATTGAAACATATCTCAGCCATATTGGATATAAAGATTTAT
1 GACTC-CTTGAACCATCTATATTC-ATTGAAACAAATCTCAGCCATATTGGATATAAAGATTT-G
* *
4433 TTTTACGAGCATCTGAATCTTGTTTCGATTTATC-TAGAAATTAATTCGTAAAAAAAATAGAAAA
63 TTTTACGAGCATCTGAATCTTCTTTCG-TTTTTCTTAGAAATTAATTCG---AAAAAA-AGAAAA
* * * * * *
4497 ACAATATTAGAAGCTTGAAAAGCCCGTCAATATTTTTGGTGTTGAGTAATATATTTTTCCTAGTA
123 ACAATATTAGAAGCGTGAAAAGCTCGTCAATCTTTTTGGTGTTGAATTATATATTTTTCTTAGTA
* * * **
4562 TTGTGGCAAAAAATTAAGAAAAAAAATTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAATTAT
188 TTGTGGGAAAAAATTAAGGAAAAAATTTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAACCAT
** * * *** * * *
4627 CAATATTTTTGGGCAAAAAACACGATT-CGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGA
253 CACGATTTTT-GACTAAAATTGCG-TTCCGGAGCCCCGGCTCTGTTTTGCATGA-----CGC--A
** * * * * *
4691 AAGACTCCTTGAAATATCTATATTTA-TGTAACCAAATCTCAGCCACAATGGAT-TTAAGAATTG
309 AAGACTCC-TGAACCATCTATATTCATTGTAA-CAAATCTCAGCCATATTGGATATAAAGATTTG
* * *
4754 CTTTTTACGAGCATCTGAATCTTCTTTCGATTTAAT-TAGAAATAAATTC-GAAAAAAAT-GGAA
372 -TTTTTACGAGCATCTGAATCTTGTTTCGATTT-ATCTAGAAATTAATTCGGAAAAAAATAGAAA
* * ** * * *
4816 AACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTATGGCGATGAATTATATATTTTTTCTTA
435 AACAATATTAGAAGCTTGAAAAGCCCGTCAATCTTTT-TGGCGTTGAATTATATA-TTTTTCTTA
* ** * * * *
4881 GTATTGTGG-AAAAAGATTGAGGATAAACTTTTCAAATCAGCTTTTTTCAAAATTTTAACCGAAA
498 GTATTGTGGCAAAAA-ATTGAAGA-AAAAATTT----TC-G-----GTCCAATTTTTAGCCGAAA
* * ** * * *
4945 TCGTGTACTAACCATCACGGTTTTTGACTAAAATTGCG-TTCCGGAGCCCCGACTCTGTTTTGC-
551 TCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGATT-CGGGGCCCCGGCTCAGTTTTGCA
* ** * * * *
5008 --A----TGGC-GCAAAGACTCCTTTAACCATCTATATTCATTGAAACAAATCTCAGCCATATTG
615 TGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTTA-TGTAACAAATCTCAGCCACAATG
* * *
5066 GATATAAAGATTTG-TTTTTACGAGCATCTGAATCTTGC-TTCGATTT-ATCTAGAAATTAATTC
678 GAT-TTAAGAATTGCTTTTTACGAGCATCTGAATCTT-CTTTCGATTTAAT-TAGAAATAAATTC
* ** * ** * * * *
5128 GTAAAAAAATAGAAAAATAATATTAGAAGCTTGAAAAGCCCGTCAATATTTTTGGTGTTGAATAA
740 G-AAAAAAAT-GGAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGGCGTTGAATTA
* *** ** **
5193 TATA-TTTTTCTTAGTATTGTGGCAAAAA-ATTCA-GA-AAA---AAAAAAT-TTC-GGTTC-AA
803 TATATTTTTTCTTAGTATTGTGG-AAAAAGATTGAGGATAAACTTTTCAAATCAGCTTTTTCAAA
** * * * ** *
5248 TTTTTAGTCGAAATCGTGTACTAACCATCACGATTTTTGGGCTAAAAACGCGATT-CGGGGCCCC
867 AGTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT-GACTAAAATTGCG-TTCCGGAGCCCC
* * *
5312 AGCTCAGTTTTGCATGATTTTCGGCAGAAA
930 GGCTCTGTTTTGCATG----GC-GC--AAA
** * * * * * * *
5342 GACTCCTTGAAATATTTATATTTA-TGTAACCAAATCTCAGCCACAATGGATATAAGGATTGGTT
1 GACTCCTTGAACCATCTATATTCATTG-AAACAAATCTCAGCCATATTGGATATAAAGATTTG-T
* ** ** * * *
5406 TTTACGAGCATCTAAATCTTCTTTCAATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGAT
64 TTTACGAGCATCTGAATCTTCTTTCGTTTTTCTTAGAAATTAATTCGAAAAAAA-GAAAAACAAT
* * *
5471 ATTAGAAGCGTGAAAA-TTCCTTCAATTTTTTTTGGTGTTGAATTATATATTTTCTCTTAGTATT
128 ATTAGAAGCGTGAAAAGCT-CGTCAA-TCTTTTTGGTGTTGAATTATATATTTT-TCTTAGTATT
* * * * *** * * * *
5535 GT-GGAACAAGATTGAGGATAAACTTTTCAAATCAGTTTTT--TC-AAA--GT-T-TTAGCCGA-
190 GTGGGAA-AAAATTAAGGAAAAAATTTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAACC-AT
* ** * *
5591 AACG-TGTACTGACTAAAATTGCGTTCCGGAGCCTCGGCTCTGTTTTGCATGGCGCAAAGACTCC
253 CACGAT-TTTTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGACGCAAAGACT-C
* * *
5655 CTGAACCATCTATATTCAATGAAACAAATCTCAGCCCTATTGGATATAAAGATTTGTTTTTACGA
316 CTGAACCATCTATATTCATTGTAACAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGA
*
5720 GCATCTCAATCTTGTTTCGATTTATCTAGAAATTAATTCGGAAAAAAATAGAAAAA-AATATTAG
381 GCATCTGAATCTTGTTTCGATTTATCTAGAAATTAATTCGGAAAAAAATAGAAAAACAATATTAG
* * * * * *
5784 AAGCTTGAAAAGCCCGTCAATCTATTTGGCATTGAATTACATTTTTTTCTTAATATTCTGGCAAA
446 AAGCTTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTCTTAGTATTGTGGCAAA
* ** * *
5849 AAATT-CAGAATAAAATTTTCAATTCAATTTTTAGCCGAAATCGTGTACTAACGATCACGATTTT
511 AAATTGAAGAA-AAAATTTTCGGTCCAATTTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
* * *
5913 TGGGCTAAAAACGCAATTCGGGGCCCCGGCTCAGTTTTGCATGACTTTTGACAGAAAGACTCCTT
575 T-GGCTAAAAACGCGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTT
* * * *
5978 GAAATATCTATATTTATGTAACCAAATCTAAGCCACAATGGTTTTAAGGATTGGTTTTTACGAGC
639 GAAATATCTATATTTATGTAA-CAAATCTCAGCCACAATGGATTTAAGAATTGCTTTTTACGAGC
* *
6043 ATCTGAATCTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGAAAAACGATATTAGAAAC
703 ATCTGAATCTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGC
* * * *
6108 ATGAAAAGTCCTTCATTTTTTTTTGGCGTTGAATTATATATTTTTTCTTAGTATTGTTGAAAAAG
768 GTGAAAAATCCTTCA-ATTTTTTTGGCGTTGAATTATATATTTTTTCTTAGTATTGTGGAAAAAG
* * * *
6173 ATTGAGGATAAACCTTTCAAATTAGCTTTTTCAAAATTTTAGCCGAAATCGTGTTCTAACCATCA
832 ATTGAGGATAAACTTTTCAAATCAGCTTTTTCAAAAGTTTAGCCGAAATCGTGTACTAACCATCA
* *
6238 CGGTTTTTGACTAAAATTGTGTTCCAGAGCCCCGGCTCTGTTTTGCATGGCGCAAA
897 CGGTTTTTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAA
* *
6294 AACTCCTTGAACCATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTCTTT
1 GACTCCTTGAACCATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTT-GTT
* * *
6359 TTTCGAGCATCTGAATCTTATTTCGATTTATC-TAGAAATTAATTCGGAAAAAAAAGAAAAACAA
65 TTACGAGCATCTGAATCTTCTTTCG-TTTTTCTTAGAAATTAATTC-G-AAAAAAAGAAAAACAA
* * * * *
6423 TAATAGAAGCTTGAAAAGCCCATCAATCTTTTTGGCGTTGAATTATATATTTTTCTTAGTATTGT
127 TATTAGAAGCGTGAAAAGCTCGTCAATCTTTTTGGTGTTGAATTATATATTTTTCTTAGTATTGT
* * * * *
6488 GGAAAAAAATTCAGAAAAAAATTTTCGGTTCATTTTTTAGCCGTAATC--G---------TCACG
192 GGGAAAAAATTAAGGAAAAAATTTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAACCATCACG
* * ** *
6542 ATTTTTGGGCAAAAAACGCGATT-CGGGGCCCCGGCT-TAGTTTTGCATGACTTTTGGCAGAAAG
257 ATTTTT-GACTAAAATTGCG-TTCCGGAGCCCCGGCTCT-GTTTTGCATGAC-----GC--AAAG
* * * * *
6605 ACTCATTAA-AATACCTATATTTA-TGTAACCAAATCTCAGCCATATTGGAT-TGAAGATTTTGT
312 ACTCCTGAACCAT--CTATATTCATTGTAA-CAAATCTCAGCCATATTGGATATAAAGA-TTTGT
*
6667 TTTTACGAGCATCTGAATCTTGTTTCGATTTAAT-TAGAAATAAATTCGGGAAAAAAATAGAAAA
373 TTTTACGAGCATCTGAATCTTGTTTCGATTT-ATCTAGAAATTAATTC-GGAAAAAAATAGAAAA
* * * * * **
6731 ACGATATTAGAAGCGTGGTAAA-TCCTTCAAT-TCTTTTGGCGTTGAATTATATACTTTTTTCCG
436 ACAATATTAGAAGC-TTGAAAAGCCCGTCAATCT-TTTTGGCGTTGAATTATATA--TTTTTCTT
* * * * * * * *
6794 ACTATTTTGGCAAAAAATTGAGGAAAAACTTTTTTTGTCAGTTTTTGCAAAATTTTAGCTGAAAT
497 AGTATTGTGGCAAAAAATTGAAGAAAAA----ATTT-TC-G---GT-CCAATTTTTAGCCGAAAT
* * * * * * * * * * *
6859 CATGTATTAACCATCACGGTTTTTGACTAAAAATGCGTTTTGGAGTCCCGACTCAATTTTGCATG
552 CGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGATTCGGGGCCCCGGCTCAGTTTTGCATG
* * * *
6924 ATTTTTGGC-GCAAAGACTCCTTGAAATATCTATATTCATCGAAACCAATCTCAGCCACATTGGA
617 ATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTTAT-GTAACAAATCTCAGCCACAATGGA
* * * * * *
6988 TATAA-AATT-TTTTTTACGAGCATCT-AATCTTGTTTCAATTTAATTAGAAATTAATTCG-GAA
680 TTTAAGAATTGCTTTTTACGAGCATCTGAATCTTCTTTCGATTTAATTAGAAATAAATTCGAAAA
* * * *
7049 AAATGGAAAAACGATATTAGAATCGTG-AAAAGCTCATCAATCTTTTTGGCGTTGAATTATATAT
745 AAATGG-AAAACGATATTAGAAGCGTGAAAAATC-CTTCAATTTTTTTGGCGTTGAATTATATAT
7113 AATTTTTTGA
Statistics
Matches: 4575, Mismatches: 737, Indels: 593
0.77 0.12 0.10
Matches are distributed among these distances:
935 7 0.00
936 26 0.01
937 2 0.00
938 1 0.00
939 1 0.00
941 53 0.01
942 38 0.01
943 90 0.02
944 41 0.01
945 28 0.01
946 2 0.00
947 57 0.01
948 67 0.01
949 4 0.00
950 37 0.01
951 115 0.03
952 263 0.06
953 508 0.11
954 151 0.03
955 389 0.09
956 686 0.15
957 233 0.05
958 75 0.02
959 132 0.03
960 79 0.02
961 56 0.01
962 41 0.01
963 164 0.04
964 113 0.02
965 114 0.02
966 67 0.01
967 97 0.02
968 138 0.03
969 85 0.02
970 228 0.05
971 118 0.03
972 190 0.04
973 1 0.00
974 2 0.00
975 2 0.00
976 5 0.00
977 58 0.01
978 11 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (952 bp):
GACTCCTTGAACCATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTGTTT
TACGAGCATCTGAATCTTCTTTCGTTTTTCTTAGAAATTAATTCGAAAAAAAGAAAAACAATATT
AGAAGCGTGAAAAGCTCGTCAATCTTTTTGGTGTTGAATTATATATTTTTCTTAGTATTGTGGGA
AAAAATTAAGGAAAAAATTTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAACCATCACGATTT
TTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGACGCAAAGACTCCTGAACCATC
TATATTCATTGTAACAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGAGCATCTGAAT
CTTGTTTCGATTTATCTAGAAATTAATTCGGAAAAAAATAGAAAAACAATATTAGAAGCTTGAAA
AGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTCTTAGTATTGTGGCAAAAAATTGAAGA
AAAAATTTTCGGTCCAATTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAAC
GCGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATA
TTTATGTAACAAATCTCAGCCACAATGGATTTAAGAATTGCTTTTTACGAGCATCTGAATCTTCT
TTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAAAATCCTT
CAATTTTTTTGGCGTTGAATTATATATTTTTTCTTAGTATTGTGGAAAAAGATTGAGGATAAACT
TTTCAAATCAGCTTTTTCAAAAGTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAA
AATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAA
Found at i:4849 original size:645 final size:642
Alignment explanation
Indices: 552--7252 Score: 8021
Period size: 645 Copynumber: 10.5 Consensus size: 642
542 TCCTTGAAAT
* * * * * *
552 ATCTATATTTA-TGTAACCAAATCTCAGCCACAATGGATAT-AGGATTTCTTTTTACGAGCATCT
1 ATCTATATTCATTG-AAACAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGAGCATCT
* * * * *
615 GAATCTTCTTTCGATTTAAT-TAGAAATAAATTC-GAAAAAAAT-GGAAAACGATATTAGAAGCG
65 GAATCTTGTTTCGATTT-ATCTAGAAATTAATTCGGAAAAAAATAGAAAAACAATATTAGAAGCT
* * * *
677 TGAAAAGTCCTTCAATTTTTTTTTGGCT-TTGAATTATATATTTTTTCTTAGTATTGTGG-AAAA
129 TGAAAAGCCCGTCAA--TCTTTTTGG-TGTTGAATAATATA-TTTTTCTTAGTATTGTGGCAAAA
* * ** * *
740 AGATTGAGGATAAAATTTTCAAATCTGCTTTTTCAAAATTTTAGCTGAAATCGTGTACTAACCAT
190 A-ATT-AAGA-AAAA-----AAAT-TTC-GGTTC-AATTTTTAGCCGAAATCGTGTACTAA-CAT
** ** * * *
805 CACGATTTTT-GAATAAAATTGCG-TTCCGGAGCCCCGGCTCTGTTTTCCA--A-----GGC-GC
243 CACGATTTTTGGGCTAAAAACGCGATT-CGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAG-
** * * * * * * *
860 AAAGACTCAC-TGAACCATCTATATTCAT-TGAAACATATCTCAGCCATATTGGATATAAAGATT
306 AAAGACTC-CTTGAAATATCTATATTTATGT-AACCAAATCTCAGCCACAATGGAT-TTAAGAAT
* * * *
923 TG-TTTTTACGAGCATCTGAATCTTGTTTCGATTT-ATCTAGAAATTAATTCGTAAAAAAAAGAA
368 TGCTTTTTACGAGCATCTGAATCTTCTTTCGATTTAAT-TAGAAATAAATTCG-AAAAAAATGGA
* * * * ** * * * * *
986 AAACAATATGAGAAACTTGAAAAGCCCGTCAATATTTTTGGTGTTGAGTAATATA-TTTTTCTTA
431 AAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTTA
* * ** * * *
1050 GTATTGTGGCAAAA-ATT-AAGA-AAAAATTT----TC-G---GTCCAATTTTTAGCCGAAATCG
496 GTATTGTGGAAAAAGATTGAGGATAAACTTTTCAAATCAGCTTTTCAAAATTTTAGCCGAAATCG
* * *** * *
1104 TGTACTAACCATCACGATTTTTGGGCTAAAAACACGATT-CGGGGCCCCGGCTCAGTTTTGCATG
561 TGTACTAACCATCACGGTTTTT-GACTAAAATTGCG-TTCCGGAGCCCCGGCTCTGTTTTGCATG
* * **
1168 ATTTTTG-GCAGAAAGAATCTTTGAAAT
624 ------GCGC--AAAGACTC-CTGAACC
* * * ** * * *
1195 ATCTATATTTA-TGTAACAAAATATCAGCCCCAATGGAT-TTAAGAATTGCTTTTTACGAGCATC
1 ATCTATATTCATTGAAAC-AAATCTCAGCCATATTGGATATAAAGATTTG-TTTTTACGAGCATC
* * * *
1258 TGAATCTTCTTTCGATTTAAT-TAGAAATAAATTC-GAAAAAAAT-GGAAAACGATATTAGAAGC
64 TGAATCTTGTTTCGATTT-ATCTAGAAATTAATTCGGAAAAAAATAGAAAAACAATATTAGAAGC
* ** * * * * * *
1320 GTGAAAAATCCTTCAATTTTTTATGGCGTTGAATTATATATTTTTTCATAATATTGTGG-AAAAC
128 TTGAAAAGCCCGTCAATCTTTT-TGGTGTTGAATAATATA-TTTTTCTTAGTATTGTGGCAAAA-
* * * ** ** ** * * *
1384 GATTGAGGATAAACTTTTCAAATCAGCTTTTTCAAAAGTTTAACGGAAATCGTGCACTAACCATC
190 AATT-AAGA-AAA-----AAAAT-TTC-GGTTC-AATTTTTAGCCGAAATCGTGTACTAA-CATC
* *** * *
1449 AC-AGTTTTT-GACTAAATTTGCG-TTCCGGAGCCCCGGCTCTGTTTTGC---A----TGGC-GC
244 ACGA-TTTTTGGGCTAAAAACGCGATT-CGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAG-
* ** * * * * * *
1503 AAAGACTCCTTTAACCATCTATATTCAT-TGAAACAAATCTCAGCCATATTGGATATAAAAATT-
306 AAAGACTCCTTGAAATATCTATATTTATGT-AACCAAATCTCAGCCACAATGGATTTAAGAATTG
* * ** * *
1566 -TGTTTTACGAGCATCTGAATCTTGTTTCGTTTTTCTTAGAAATTAATTC-AGAAAAAATAGAAA
370 CT-TTTTACGAGCATCTGAATCTTCTTTCGATTTAATTAGAAATAAATTCGA-AAAAAAT-GGAA
* * * * * * * *
1629 AACAATATTAGAAGCTTG-AAAAGCTCGTCAATATTTTTGGTGTTGAATAACATA-TTTTTCTTA
432 AACGATATTAGAAGCGTGAAAAATC-CTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTTA
* ** * *
1692 GTATTGTGGCGAAAAA-ATTAAGGA-AAA-TTTT----TTTG--GTTC--AATTTATAGCTGAAA
496 GTATTGT-G-GAAAAAGATTGAGGATAAACTTTTCAAATCAGCTTTTCAAAATTT-TAGCCGAAA
1746 TCGTGTACTAACCATCACGGTTTTTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCAT
558 TCGTGTACTAACCATCACGGTTTTTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCAT
*
1811 GACGCAAAGACTCACTGAACC
623 GGCGCAAAGACTC-CTGAACC
* * *
1832 ATCTATATTCATTGGAACAAATCTCAACCATATTGGATATTAAGATTTGTTTTTACGAGCATCTG
1 ATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGAGCATCTG
* *
1897 AATCTTTTTTCGATTTATCTAGAAATTAATTTGGAAAAAAATAGAAAAACAATATTAGAAGCTTG
66 AATCTTGTTTCGATTTATCTAGAAATTAATTCGGAAAAAAATAGAAAAACAATATTAGAAGCTTG
* * * * * *
1962 AAAAGCGCGTCAATCTTTTTGGCGTTGAATTACATATTTTTCTTAGTATTGTGGCAAAAAAATCA
131 AAAAGCCCGTCAATCTTTTTGGTGTTGAATAATATATTTTTCTTAGTATTGTGGCAAAAAATTAA
* * * * *
2027 GAAAAAAATTTTCGGTTCAATTTTTAGTCGAAATCGTG---T-AC-GCACGAGTTTTAGGCTAAA
196 GAAAAAAAATTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAACATCACGATTTTTGGGCTAAA
* *
2087 AACACGATTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCT
261 AACGCGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCT
*
2152 ATATTTATGTAACCAAATCTCAGCCACAATGGATTTAGGAATTGCTTTTTACGAGCATCTGAATC
326 ATATTTATGTAACCAAATCTCAGCCACAATGGATTTAAGAATTGCTTTTTACGAGCATCTGAATC
2217 TTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAAAAT
391 TTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAAAAT
*
2282 CCTTCAATTTTTTATGGTGTTGAATTATATATTTTTTCTTAGTATTGTGGAAAAAGATTGAGGAT
456 CCTTCAATTTTTT-TGGCGTTGAATTATATATTTTTTCTTAGTATTGTGGAAAAAGATTGAGGAT
* * *
2347 AAACTTTACAAATCAGCTTTTTCAAAAGTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTG
520 AAACTTTTCAAATCAGC-TTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
*
2412 ACTAAAATTGCGTTCCGGAGCCCCAGCTCTGTTTTGCATGGCGCAAAGACTCACTGAACC
584 ACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAAGACTC-CTGAACC
2472 ATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGAGCATCTG
1 ATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGAGCATCTG
* * * * *
2537 AATCTTGTTTCGATTTATCTAGAAATTAATTCGTAAAAAAAATAGAAAATCATTATTAGTAGCAT
66 AATCTTGTTTCGATTTATCTAGAAATTAATTCG-GAAAAAAATAGAAAAACAATATTAGAAGCTT
2602 GAAAAGCCCGTCAATCTTTTTGGTGTTGAATAATATATTTTTCTTAGTATTGTGGCAAAAAATTA
130 GAAAAGCCCGTCAATCTTTTTGGTGTTGAATAATATATTTTTCTTAGTATTGTGGCAAAAAATTA
* * *
2667 AGAAAAAAATTTTCGGTTCAATTTTTAGCGGAAATCGTGTACTAACCATCATGATTTTTGGGCTA
195 AGAAAAAAAATTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAA-CATCACGATTTTTGGGCTA
*
2732 AAAACGCGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAAAAAGACTCCTTGAAATAT
259 AAAACGCGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATAT
* * * *
2797 CAATATTT-TAGTATCCAAATCTCAGCCACAATGGATTTAAGGATTTCTTTTTACGAGCATCTGA
324 CTATATTTAT-GTAACCAAATCTCAGCCACAATGGATTTAAGAATTGCTTTTTACGAGCATCTGA
** * *
2861 ATCTTCTTTCGATTTAAACAGAAATAAATTCGAAAAAAATGGAAAATGATATTAGAAGTGTGAAA
388 ATCTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAA
* *
2926 AATCCTTCAATTTTTCTGGCGTTAAATTATATATTTTTTCTTAGTATTGTGGAAAAAGATTGAGG
453 AATCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTTAGTATTGTGGAAAAAGATTGAGG
* *
2991 ATAAAATTTTCAAATCAGCTTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
518 ATAAACTTTTCAAATCAGC-TTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTT
3056 TGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAAGACTCACTGAACC
582 TGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAAGACTC-CTGAACC
*
3118 ATCTATATTCATTGAAACATATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGAGCATCTG
1 ATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGAGCATCTG
* *
3183 AATCTTGTTTCGATTTATATAGAAATTAATTCGTAAAAAAATAGAAAAACAATATTAGAAGCTTG
66 AATCTTGTTTCGATTTATCTAGAAATTAATTCGGAAAAAAATAGAAAAACAATATTAGAAGCTTG
* *
3248 AAAAGCCCGTCAATGTTTTTGGTGTTGAGTAATATATTTTTCTTAGTATTGTGGCAAAAAATTAA
131 AAAAGCCCGTCAATCTTTTTGGTGTTGAATAATATATTTTTCTTAGTATTGTGGCAAAAAATTAA
* * * *
3313 G-AAAAAAATTTCGGTCCAATTTTTAGCCAAAATCGTGTATTAACCATCACGATTTTTGGGCAAA
196 GAAAAAAAATTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAA-CATCACGATTTTTGGGCTAA
* * *
3377 AAACACGATTCGGGGCCCCGGCTAAGTTTTGCATGATTCTT--------GA---CTTGAAATATC
260 AAACGCGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATC
* *
3431 TATATTTATGTAACAAAATCTCAGCCCCAATGGATTTAAGAATTGCTTTTTACGAGCATCTGAAT
325 TATATTTATGTAACCAAATCTCAGCCACAATGGATTTAAGAATTGCTTTTTACGAGCATCTGAAT
3496 CTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAAAA
390 CTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAAAA
*
3561 TCCTTCAATCTTTTATGGCGTTGAATTATATATTTTTTCTTAGTATTGTGGAAAAAGATTGAGGA
455 TCCTTCAAT-TTTTTTGGCGTTGAATTATATATTTTTTCTTAGTATTGTGGAAAAAGATTGAGGA
* * * *
3626 TACACTTTACAAATCAGCTTTTCAAAAGTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTG
519 TAAACTTTTCAAATCAGCTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
*
3691 ACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAAGACTCCTTTAACC
584 ACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAAGACTCC-TGAACC
* * *
3751 ATCTATATTCATTGGAACAAATCTCAACCATATTGGATATAAAAATTTG-TTTTACGAGCATCTG
1 ATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGAGCATCTG
*
3815 AATCTTGTTTCGTTTTATCTAGAAATTAATTCGGAAAAAAATAGAAAAACAATATTAGAAGCTTG
66 AATCTTGTTTCGATTTATCTAGAAATTAATTCGGAAAAAAATAGAAAAACAATATTAGAAGCTTG
* * *
3880 AAAAGCTCGTCAATCTTTTTGGTGTTGAATAACATATTTTTCTTAGTATTGTGGCAAAAAATTCA
131 AAAAGCCCGTCAATCTTTTTGGTGTTGAATAATATATTTTTCTTAGTATTGTGGCAAAAAATTAA
*
3945 GAAAAAAAATTTTCGGTTCAATTTTTAGCGGAAATCGTG--------T---GATTTTTGGGCTAA
196 GAAAAAAAA-TTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAACATCACGATTTTTGGGCTAA
* * * * * *
3999 AAACGCGATTCGTGGTCTCGGCTCAGTTTTGTATGATTGTTGGCAAAAAGACTCCTTGAAATATC
260 AAACGCGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATC
* * * *
4064 TATATTTATCTAACCAAATCTCAGCCACAATGGATTTAAGGATTTCTTTTTACGAGCATTTGAAT
325 TATATTTATGTAACCAAATCTCAGCCACAATGGATTTAAGAATTGCTTTTTACGAGCATCTGAAT
* *
4129 CTTCTTTCGATTTAAATAGAAATAAATTCGAAAAAAAAGGAAAACGATATTAGAAGCGTGAAAAA
390 CTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAAAA
4194 TCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTTAGTATTGTGGAAAAAGATTGAGGAT
455 TCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTTAGTATTGTGGAAAAAGATTGAGGAT
*
4259 AAACTTTTCAAATCAGCTTTTCAAAATTTTAGCCGAAATCTTGTACTAACCATCACGGTTTTTGA
520 AAACTTTTCAAATCAGCTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGA
4324 CTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAAGACTCACTGAACC
585 CTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAAGACTC-CTGAACC
* *
4383 ATCTATA-TCAATTGAAACATATCTCAGCCATATTGGATATAAAGATTTATTTTTACGAGCATCT
1 ATCTATATTC-ATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGAGCATCT
*
4447 GAATCTTGTTTCGATTTATCTAGAAATTAATTCGTAAAAAAAATAGAAAAACAATATTAGAAGCT
65 GAATCTTGTTTCGATTTATCTAGAAATTAATTCG-GAAAAAAATAGAAAAACAATATTAGAAGCT
* * *
4512 TGAAAAGCCCGTCAATATTTTTGGTGTTGAGTAATATATTTTTCCTAGTATTGTGGCAAAAAATT
129 TGAAAAGCCCGTCAATCTTTTTGGTGTTGAATAATATATTTTTCTTAGTATTGTGGCAAAAAATT
* ** *
4577 AAGAAAAAAAATTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAATTATCAATATTTTTGGGCA
194 AAGAAAAAAAATTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAA-CATCACGATTTTTGGGCT
*
4642 AAAAACACGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATA
258 AAAAACGCGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATA
4707 TCTATATTTATGTAACCAAATCTCAGCCACAATGGATTTAAGAATTGCTTTTTACGAGCATCTGA
323 TCTATATTTATGTAACCAAATCTCAGCCACAATGGATTTAAGAATTGCTTTTTACGAGCATCTGA
4772 ATCTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAA
388 ATCTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAA
*
4837 AATCCTTCAATTTTTTATGGCGATGAATTATATATTTTTTCTTAGTATTGTGGAAAAAGATTGAG
453 AATCCTTCAATTTTTT-TGGCGTTGAATTATATATTTTTTCTTAGTATTGTGGAAAAAGATTGAG
*
4902 GATAAACTTTTCAAATCAGCTTTTTTCAAAATTTTAACCGAAATCGTGTACTAACCATCACGGTT
517 GATAAACTTTTCAAATCAGC--TTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTT
* *
4967 TTTGACTAAAATTGCGTTCCGGAGCCCCGACTCTGTTTTGCATGGCGCAAAGACTCCTTTAACC
580 TTTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAAGACTCC-TGAACC
5031 ATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGAGCATCTG
1 ATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGAGCATCTG
* * *
5096 AATCTTGCTTCGATTTATCTAGAAATTAATTCGTAAAAAAATAGAAAAATAATATTAGAAGCTTG
66 AATCTTGTTTCGATTTATCTAGAAATTAATTCGGAAAAAAATAGAAAAACAATATTAGAAGCTTG
*
5161 AAAAGCCCGTCAATATTTTTGGTGTTGAATAATATATTTTTCTTAGTATTGTGGCAAAAAATTCA
131 AAAAGCCCGTCAATCTTTTTGGTGTTGAATAATATATTTTTCTTAGTATTGTGGCAAAAAATT-A
* *
5226 GAAAAAAAAAATTTCGGTTCAATTTTTAGTCGAAATCGTGTACTAACCATCACGATTTTTGGGCT
195 -AGAAAAAAAATTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAA-CATCACGATTTTTGGGCT
* *
5291 AAAAACGCGATTCGGGGCCCCAGCTCAGTTTTGCATGATTTTCGGCAGAAAGACTCCTTGAAATA
258 AAAAACGCGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATA
* * * * *
5356 TTTATATTTATGTAACCAAATCTCAGCCACAATGGATATAAGGATTGGTTTTTACGAGCATCTAA
323 TCTATATTTATGTAACCAAATCTCAGCCACAATGGATTTAAGAATTGCTTTTTACGAGCATCTGA
*
5421 ATCTTCTTTCAATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAA
388 ATCTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAA
* * * *
5486 ATTCCTTCAATTTTTTTTGGTGTTGAATTATATATTTTCTCTTAGTATTGTGGAACAAGATTGAG
453 AATCCTTCAA-TTTTTTTGGCGTTGAATTATATATTTTTTCTTAGTATTGTGGAAAAAGATTGAG
* *
5551 GATAAACTTTTCAAATCAGTTTTTTCAAAGTTTTAGCCGAAA-CGTG---------T-AC-----
517 GATAAACTTTTCAAATCAG-CTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
*
5600 -TGACTAAAATTGCGTTCCGGAGCCTCGGCTCTGTTTTGCATGGCGCAAAGACTCCCTGAACC
581 TTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAAGACT-CCTGAACC
* * *
5662 ATCTATATTCAATGAAACAAATCTCAGCCCTATTGGATATAAAGATTTGTTTTTACGAGCATCTC
1 ATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGAGCATCTG
5727 AATCTTGTTTCGATTTATCTAGAAATTAATTCGGAAAAAAATAGAAAAA-AATATTAGAAGCTTG
66 AATCTTGTTTCGATTTATCTAGAAATTAATTCGGAAAAAAATAGAAAAACAATATTAGAAGCTTG
* ** * * * * * *
5791 AAAAGCCCGTCAATCTATTTGGCATTGAATTACATTTTTTTCTTAATATTCTGGCAAAAAATTCA
131 AAAAGCCCGTCAATCTTTTTGGTGTTGAATAATATATTTTTCTTAGTATTGTGGCAAAAAATTAA
* * **
5856 GAATAAAATTTTCAATTCAATTTTTAGCCGAAATCGTGTACTAACGATCACGATTTTTGGGCTAA
196 GAAAAAAAATTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAAC-ATCACGATTTTTGGGCTAA
* * *
5921 AAACGCAATTCGGGGCCCCGGCTCAGTTTTGCATGACTTTTGACAGAAAGACTCCTTGAAATATC
260 AAACGCGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATC
* * * *
5986 TATATTTATGTAACCAAATCTAAGCCACAATGGTTTTAAGGATTGGTTTTTACGAGCATCTGAAT
325 TATATTTATGTAACCAAATCTCAGCCACAATGGATTTAAGAATTGCTTTTTACGAGCATCTGAAT
* * * *
6051 CTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGAAAAACGATATTAGAAACATGAAAAG
390 CTTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAAAA
* *
6116 TCCTTCATTTTTTTTTGGCGTTGAATTATATATTTTTTCTTAGTATTGTTGAAAAAGATTGAGGA
455 TCCTTCA-ATTTTTTTGGCGTTGAATTATATATTTTTTCTTAGTATTGTGGAAAAAGATTGAGGA
* * *
6181 TAAACCTTTCAAATTAGCTTTTTCAAAATTTTAGCCGAAATCGTGTTCTAACCATCACGGTTTTT
519 TAAACTTTTCAAATCAGC-TTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT
* * *
6246 GACTAAAATTGTGTTCCAGAGCCCCGGCTCTGTTTTGCATGGCGCAAAAACTCCTTGAACC
583 GACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAAGACTCC-TGAACC
* *
6307 ATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTCTTTTTTCGAGCATCTG
1 ATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGAGCATCTG
* *
6372 AATCTTATTTCGATTTATCTAGAAATTAATTCGGAAAAAAA-AGAAAAACAATAATAGAAGCTTG
66 AATCTTGTTTCGATTTATCTAGAAATTAATTCGGAAAAAAATAGAAAAACAATATTAGAAGCTTG
* * * * *
6436 AAAAGCCCATCAATCTTTTTGGCGTTGAATTATATATTTTTCTTAGTATTGTGGAAAAAAATTCA
131 AAAAGCCCGTCAATCTTTTTGGTGTTGAATAATATATTTTTCTTAGTATTGTGGCAAAAAATTAA
* * * *
6501 GAAAAAAATTTTCGGTTCATTTTTTAGCCGTAATC--G--------TCACGATTTTTGGGCAAAA
196 GAAAAAAAATTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAACATCACGATTTTTGGGCTAAA
* * * * *
6556 AACGCGATTCGGGGCCCCGGCTTAGTTTTGCATGACTTTTGGCAGAAAGACTCATTAAAATACCT
261 AACGCGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCT
* * * *
6621 ATATTTATGTAACCAAATCTCAGCCATATTGGATTGAAGATTTTG-TTTTTACGAGCATCTGAAT
326 ATATTTATGTAACCAAATCTCAGCCACAATGGATTTAAGA-ATTGCTTTTTACGAGCATCTGAAT
* * **
6685 CTTGTTTCGATTTAATTAGAAATAAATTCGGGAAAAAAATAGAAAAACGATATTAGAAGCGTGGT
390 CTTCTTTCGATTTAATTAGAAATAAATTC--GAAAAAAAT-GGAAAACGATATTAGAAGCGTGAA
* ** * *
6750 AAATCCTTCAATTCTTTTGGCGTTGAATTATATACTTTTTTCCGACTATTTTGGCAAAAA-ATTG
452 AAATCCTTCAATTTTTTTGGCGTTGAATTATATA-TTTTTTCTTAGTATTGTGG-AAAAAGATTG
* **** * * * *
6814 AGGAAAAACTTTTTTTGTCAGTTTTTGCAAAATTTTAGCTGAAATCATGTATTAACCATCACGGT
515 AGGATAAACTTTTCAAATCAGCTTTT-CAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGT
* ** * * **
6879 TTTTGACTAAAAATGCGTTTTGGAGTCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCC
579 TTTTGACTAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGC---A----TGGCGCAAAGACTCC
**
6944 TTGAAAT
637 -TGAACC
* * *
6951 ATCTATATTCATCGAAACCAATCTCAGCCACATTGGATATAAA-ATTT-TTTTTACGAGCATCT-
1 ATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGAGCATCTG
* * * * *
7013 AATCTTGTTTCAATTTAAT-TAGAAATTAATTCGG--AAAAATGGAAAAACGATATTAGAATCGT
66 AATCTTGTTTCGATTT-ATCTAGAAATTAATTCGGAAAAAAATAGAAAAACAATATTAGAAGCTT
* * * * * *
7075 GAAAAGCTCATCAATCTTTTTGGCGTTGAATTATATATAATTTTT-TGAGTATTTTGACCAAAAA
130 GAAAAGCCCGTCAATCTTTTTGGTGTTGAA-TA-ATAT-ATTTTTCTTAGTATTGTG-GC-AAAA
* * * * * * *
7139 AATTGAGAAAAAAAATTTCGGGTCAGTTATTAGCCGAAATTGTGTACTAACCATCATGGTTTTT-
190 AATTAAGAAAAAAAATTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAA-CATCACGATTTTTG
*** * * *
7203 TATTAGAAACGC-ATTCCGGGGCCACGGCTCTGTTTTGCATGATTTTTGGC
254 GGCTAAAAACGCGATT-CGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGC
7253 GTCGAGACTC
Statistics
Matches: 5412, Mismatches: 478, Indels: 325
0.87 0.08 0.05
Matches are distributed among these distances:
621 7 0.00
622 76 0.01
623 3 0.00
624 1 0.00
625 2 0.00
627 16 0.00
628 335 0.06
629 95 0.02
630 153 0.03
631 188 0.03
632 356 0.07
633 509 0.09
634 352 0.07
635 6 0.00
636 43 0.01
637 226 0.04
638 50 0.01
639 45 0.01
640 232 0.04
641 167 0.03
642 153 0.03
643 237 0.04
644 340 0.06
645 595 0.11
646 336 0.06
647 304 0.06
648 213 0.04
649 317 0.06
650 6 0.00
653 3 0.00
654 37 0.01
655 9 0.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (642 bp):
ATCTATATTCATTGAAACAAATCTCAGCCATATTGGATATAAAGATTTGTTTTTACGAGCATCTG
AATCTTGTTTCGATTTATCTAGAAATTAATTCGGAAAAAAATAGAAAAACAATATTAGAAGCTTG
AAAAGCCCGTCAATCTTTTTGGTGTTGAATAATATATTTTTCTTAGTATTGTGGCAAAAAATTAA
GAAAAAAAATTTCGGTTCAATTTTTAGCCGAAATCGTGTACTAACATCACGATTTTTGGGCTAAA
AACGCGATTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCT
ATATTTATGTAACCAAATCTCAGCCACAATGGATTTAAGAATTGCTTTTTACGAGCATCTGAATC
TTCTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAACGATATTAGAAGCGTGAAAAAT
CCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTTAGTATTGTGGAAAAAGATTGAGGATA
AACTTTTCAAATCAGCTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGAC
TAAAATTGCGTTCCGGAGCCCCGGCTCTGTTTTGCATGGCGCAAAGACTCCTGAACC
Done.