Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005735.1 Corchorus capsularis cultivar CVL-1 contig05753, 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: 11827
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:567 original size:14 final size:14
Alignment explanation
Indices: 542--571 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
532 ATATATATAT
*
542 ATATATATAATAAA
1 ATATATAAAATAAA
556 ATATATAAAATAAA
1 ATATATAAAATAAA
570 AT
1 AT
572 TACCACTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATATAAAATAAA
Found at i:1492 original size:49 final size:53
Alignment explanation
Indices: 1376--1492 Score: 138
Period size: 53 Copynumber: 2.3 Consensus size: 53
1366 TTCGAGGCTC
* * *
1376 AAAATTAGTCAAAAATCCAAAGGCATTACAATTCACAACCCTCTCTCGGGGTC
1 AAAATTGGCCAAAAATCCAAAGGCATTACAATTCACAACCCTCTCTCGGGGTA
*
1429 AAAATTGGCCAAAAATCCAAAGGC-TTAACCA-TCACAA-CCT-T-T-GTGGGTA
1 AAAATTGGCCAAAAATCCAAAGGCATT-ACAATTCACAACCCTCTCTCG-GGGTA
1478 AAAATTGGCCAAAAA
1 AAAATTGGCCAAAAA
1493 ATTGAAGGCT
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
48 1 0.02
49 20 0.34
50 1 0.02
51 3 0.05
52 8 0.14
53 25 0.43
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (53 bp):
AAAATTGGCCAAAAATCCAAAGGCATTACAATTCACAACCCTCTCTCGGGGTA
Found at i:1980 original size:48 final size:48
Alignment explanation
Indices: 1906--1997 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
1896 CACAAAAGCA
* *
1906 AAAGATTAACCATCATGGCTAAGGGGGG-CAAAAAGTGGCCAAAATGTC
1 AAAGACTAACCATCATGACTAAGGGGGGTC-AAAAGTGGCCAAAATGTC
* *
1954 AAAGACTAACCATCACT-ACTATGGGGGGTCAAAATTGGCCAAAA
1 AAAGACTAACCATCA-TGACTAAGGGGGGTCAAAAGTGGCCAAAA
1998 ATTCCTAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 36 0.95
49 2 0.05
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.17
Consensus pattern (48 bp):
AAAGACTAACCATCATGACTAAGGGGGGTCAAAAGTGGCCAAAATGTC
Found at i:7419 original size:21 final size:20
Alignment explanation
Indices: 7390--7428 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
7380 ATGATTATTT
*
7390 TTTTGAAATATATGTTGTTA
1 TTTTGAAATATAAGTTGTTA
*
7410 TTTTGTAAATCTAAGTTGT
1 TTTTG-AAATATAAGTTGT
7429 AGATCTAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (20 bp):
TTTTGAAATATAAGTTGTTA
Found at i:9914 original size:646 final size:644
Alignment explanation
Indices: 7498--11437 Score: 5398
Period size: 646 Copynumber: 6.1 Consensus size: 644
7488 ATATCTAAAA
* * * * **
7498 TGAAATATTTCTATTCATCGAACCAAATCTCAGTCACATTGGATTTAAAGATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
* * * * *
7563 CATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCG-GAAAAAATAGGAAAACTATATTGGA
66 CATCTGAAATGTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGGAAAACGATATTGGA
* *** * * * * *
7627 AGCGTGAAAAACCCTTCAATTTTTTTTTTGCGTTAAATTATATA-TTATTCCGAGTATTGTGGCA
131 AGCGTTAAAAACCCTTCAA--TTTTTTAAAC-ATCAATTATATATTTTTTCCCAGTATTGTGGTA
* * ***** * * *
7691 AAAATATCAGAAATTTTTTTTTCAGGTAAATTCTTA-CTCGAAATCGTGTACTAACCATCACTGT
193 AAAATTTTAGAAAAAAAGTTTTCGGGTCAATTCTTAGC-CGAAATCGTGTACTAACCATCACTAT
* * * * *
7755 TAATGGGCTAAAAACGCGTTTCGGGACCCTGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTC
257 TATTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCATAAAGCCTC
* * * * * * * * *
7820 CTAGAAATATCTCTATTCATCGAAACAAATCTAAGCCAAATTGGATTTAAGAATTTATTTTTACG
322 CTTGAAATATCTCTATTCATTGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACG
* * * * * *
7885 AGCATCTGAATTTTGTTCCGATTTAATTAGAAATAAATTCGGAAAAAATGGGAAAACGATATTAG
387 AGCATCTGAAATGTGTTTCGATTT-ATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGG
* * ** * * * *
7950 AAACGTGAAAAACCCTTCAATATTTTT-T-TGTTAAATTATATATTTTTT-CGAGTATTCTGGCA
451 AAGCGTTAAAAACCCTTCAAT-TTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTA
* * * **
8012 AAAATTTCA-AAAAAAAGTTTCGGGTCAATTCTTAGGCGAAATCGTGTACTAACCATCACTGTTA
515 AAATTTTCAGAAAAAAATTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACAATTA
* * * * * ** * * * *
8076 TTGGGCTAAAAACGCGTTTCGGGGCCACGACTCAGTTTTGCGTGATTTTTGGAAGAAAGCCTTCT
580 TAGGGCTAAAAACGCGTTTCGGGGCCCCGCCTCAGTTTTCCATGATTTTCAGCATAAAGCGTCCT
* * * *
8141 TGAAATATCTCTATTCATCGAACCAAATATCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
* * * * *
8206 CATCT-AATTTTTTTTTCGATTTAATTAGAAATAAATTCGGGAAAAAAATGGGGAAACGATATTG
66 CATCTGAA-ATGTGTTTCGATTTAATTAGAAATAAATTC-GAAAAAAAATGGGAAAACGATATTG
* * * *
8270 GAAGTGTGAAAAACCCTTCAATTTCTTAAACATTCAATTATATATTTTTTCCAAGTATTGTGGTA
129 GAAGCGTTAAAAACCCTTCAATTTTTTAAACA-TCAATTATATATTTTTTCCCAGTATTGTGGTA
* * * * *
8335 AAAATTTCATG-AAAAAATTTTTCGGGTCAATTCTTAGCCGAAATCGTGCACGTTACCATCACTG
193 AAAATTTTA-GAAAAAAAGTTTTCGGGTCAATTCTTAGCCGAAATCGTGTAC-TAACCATCACTA
* * * * *
8399 TTATTGGGCTAAAAACGCATTTCGGGGCCCCGACTCAGTTTTTCATGATTTTTGGCAGAAAGCCT
256 TTATTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCATAAAGCCT
* * * * * * **
8464 CCTTGAAATATTTCTATTTATAGAACCAAATCTCAGCCATATTGGATTTAAAGATTTGTTTTTAC
321 CCTTGAAATATCTCTATTCATTGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTAC
* * *
8529 GAGCATCTG-AATTTAGTTTCGATTTAATT-AAAAAAATTCGAAAAAAATGGGAAAACGATATTG
386 GAGCATCTGAAATGT-GTTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTG
* * * * *
8592 GAAGTGTGAAAAACCCTTCAATTTCTTAAACATTCAATTATATA-TTTTTCCAAGTATTGTGGTA
450 GAAGCGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTA
* * * * **
8656 AAAATTTCATGAAAAAATTTTTCGGGTCAATTCTTAGACGAAATCGTGTACGTTACCATCACTGT
515 AAATTTTCA-GAAAAAAATTTTCGGGTCAATTCTTAGCCGAAATCGTGTAC-TAACCATCACAAT
* * * * ** * * *
8721 TATTGGGCTAAAAACGCGTTTCGTGGCCACGGCTCAGTTCTT-CATGATTTTTGGCAGAAAACCT
578 TATAGGGCTAAAAACGCGTTTCGGGGCCCCGCCTCAGTT-TTCCATGATTTTCAGCATAAAGCGT
8785 CCT
642 CCT
* * * *
8788 TGAAATATCCCTATTTATTGAATCAAATCTCAGTCACATAGGATTTATGGATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
* *
8853 CATCTGAAATGTGTTTCGATTT-ATTTGAAATAAATTCG-AAAAAAATAGGAAAACGATATTGGA
66 CATCTGAAATGTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGGAAAACGATATTGGA
* ** *
8916 ATCGTTAAAAACCCTTCAA-TTTTTAAACATTCAATTATATATTTTTTCCTTGTGTTGTGGTAAA
131 AGCGTTAAAAACCCTTCAATTTTTTAAACA-TCAATTATATATTTTTTCCCAGTATTGTGGTAAA
8980 AATTTTAG-AAAAAAGTTTTCGGGTCAATTCTTAGCCGAAATCGTGTACT--CCATCACTATTAT
195 AATTTTAGAAAAAAAGTTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACTATTAT
*
9042 TGGGCTAAAAACGCGTTTCGGGG-CCCGGCTCAGTTTTGTATGATTTTCGGCATAAAGCCTCCTT
260 TGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCATAAAGCCTCCTT
*
9106 GAAATATCTCTATTCATTGAATCAATTCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAGC
325 GAAATATCTCTATTCATTGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAGC
9171 ATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAAGC
390 ATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAAGC
* *
9236 GTTAAAAACCCTTCAAATTTTTATATATTCAATTATATATTTTTTCCTAGTATTGTGGTAAAATT
455 GTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTAAAATT
* * * *
9301 TTCAGAAAAAAATTTTTCGGGTCAATTCTTAGCCGGAATCGTATACTTAACCATCACTATTATTG
520 TTCAGAAAAAAA-TTTTCGGGTCAATTCTTAGCCGAAATCGTGTAC-TAACCATCACAATTATAG
* * * * *
9366 GGCTAAAAACGAGTTTTGGGGTCCCGGCTCAGTTTTCCATGATTTTCGGCATAAAGCGTCCT
583 GGCTAAAAACGCGTTTCGGGGCCCCGCCTCAGTTTTCCATGATTTTCAGCATAAAGCGTCCT
* *
9428 TGAAATATCTCTATTCATTGAATCAATTCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
* *
9493 CATCTGAAATGTGTTTTGATTT-ATTTGAAATAAATTCGAAAAAAAATGGGAAAACGATATTGGA
66 CATCTGAAATGTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGGAAAACGATATTGGA
*
9557 AGCATTAAAAACCCTTCAATTTTTTATAAACA-CAATTATATATTTTTTCCCAGTATTGTGGTAA
131 AGCGTTAAAAACCCTTCAA-TTTTT-TAAACATCAATTATATATTTTTTCCCAGTATTGTGGTAA
* * *
9621 AAATTTTAGAAAAAAAGTTTTCGGGTCAATTCTTAACCGAAATCGTGTACTAATCATCACTGTTA
194 AAATTTTAGAAAAAAAGTTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACTATTA
*
9686 TTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGAATGATTTTCGGCATAAAGCCTCCT
259 TTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCATAAAGCCTCCT
*
9751 TGAAATATCTCTATTCATTGAATCAAATCTCAGCCACATAGGAATTATGGATTTGTTTTTACGAG
324 TGAAATATCTCTATTCATTGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
*
9816 CATCTGAAATGTGGTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAAG
389 CATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAAG
* * *
9881 CGTTAAAACCCCTTCAATTTTTTATACATTCAATTCTATATTTTTTCCTAGTATTGTGGTAAGAT
454 CGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTAAAAT
* *
9946 TTTCATAAAAAAAAATTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACAATTATAG
519 TTTCA-GAAAAAAATTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACAATTATAG
* * * *
10011 AGCTGAAAACGCGTTTCGGGGCCCCACCTCAGTTTTCCATGATTTTCAACATAAAGCGTCCT
583 GGCTAAAAACGCGTTTCGGGGCCCCGCCTCAGTTTTCCATGATTTTCAGCATAAAGCGTCCT
* * *
10073 TGAAATATCTCTATTCATCGAACCAAATCTCAGCCTCATAGGATTTATGGATTTGTTTCTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
* * * * * *
10138 CATATG-ATTTTTTTTCGATTTAATTAGAAATAAATTC-AGAAAAAATGGGAAAACGATATTAGA
66 CATCTGAAATGTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGGAAAACGATATTGGA
** *
10201 AGCGTTAAAAACCCTTCAA-TTTTTAAACATTCAATTATATATTTTTTCCTTGTGTTGTGGTAAA
131 AGCGTTAAAAACCCTTCAATTTTTTAAACA-TCAATTATATATTTTTTCCCAGTATTGTGGTAAA
* * *
10265 AATTTTAGAAAAAAAGTTTTCTGGTCAATTCTTAGCCGAAATCGTGTAGTAATAATCATCACTAT
195 AATTTTAGAAAAAAAGTTTTCGGGTCAATTCTTAGCCGAAATC--GT-GTACTAACCATCACTAT
**
10330 TATTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTAAATGATTTTCGGCATAAAGCCTC
257 TATTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCATAAAGCCTC
10395 CTTGAAATATCTCTATTCATTGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACG
322 CTTGAAATATCTCTATTCATTGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACG
*
10460 AGCATCTGAAATGTGTTTCGATTTATTTGAAAGAAATTCGAAAAAAAATGGGAAAACGATATTGG
387 AGCATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCG-AAAAAAATGGGAAAACGATATTGG
* * *
10525 AAGCGTTAAAAATCCTTCAATGTTTTATACATTCAATTCTATATTTTTTCCTAGTATTGTGGTAA
451 AAGCGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTAA
* *
10590 GATTTTCAGAAAAAAAAAAAATTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACAA
516 AATTTTCAG----AAAAAAATTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACAA
10655 TTATAGGGCTAAAAACGCGTTTCGGGGCCCCGCCTCAGTTTTCCATGATTTTCAGCATAAAGCGT
577 TTATAGGGCTAAAAACGCGTTTCGGGGCCCCGCCTCAGTTTTCCATGATTTTCAGCATAAAGCGT
10720 CCT
642 CCT
*
10723 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCTCATAGGATTTATGGATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
*
10788 CATCTGAAATGTGTTTCGATTT-ATTTGAAATAAATTCGAAAAAAAAATGGGAAAACGATATTGG
66 CATCTGAAATGTGTTTCGATTTAATTAGAAATAAATTCG-AAAAAAAATGGGAAAACGATATTGG
*
10852 AAGCGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCCAGTATTGTGGT-A
130 AAGCGTTAAAAACCCTTCAATTTTTTAAACA-TCAATTATATATTTTTTCCCAGTATTGTGGTAA
* ** * *
10916 AAATTTTCAGAAAAAAATTTTTCAAGTAAATTCTTAGCCGAAATCGTGTACTAACCATCACAATT
194 AAATTTT-AGAAAAAAAGTTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACTATT
* * * * * *
10981 ATAGGGCTAAAAACGCGTTTCGGGGCCCCGCCTCAGTTTTCCATGATTTTCAGCATAAAGCGTTC
258 ATTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCATAAAGCCTCC
* *
11046 TTGAAATATCTCTATTCATCGAATCAAATCTCAGCCTCATAGGATTTATGGATTTGTTTTTACGA
323 TTGAAATATCTCTATTCATTGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGA
*
11111 GCATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAT
388 GCATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAA
** * * * *
11176 GATTTAAAAACCCTTCAATTTTTTATAAATTCAATTCTATA-TTTTTCTTAGTATTGTGGTAAGA
453 GCGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTAAAA
11240 TTTTCAGAAAAAAATTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACAATTATAG
518 TTTTCAGAAAAAAATTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACAATTATAG
11305 GGCTAAAAACGCGTTTCGGGGCCCCGCCTCAGTTTTCCATGATTTTCAGCATAAAGCGTCCT
583 GGCTAAAAACGCGTTTCGGGGCCCCGCCTCAGTTTTCCATGATTTTCAGCATAAAGCGTCCT
* ** *
11367 TGAAATATCTCTATTCATCGAATCAAATCTCAACCTTATAGGATTTATGAATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
11432 CATCTG
66 CATCTG
11438 TTCGGGTCAA
Statistics
Matches: 3000, Mismatches: 250, Indels: 93
0.90 0.07 0.03
Matches are distributed among these distances:
638 110 0.04
639 118 0.04
640 221 0.07
641 48 0.02
642 87 0.03
643 329 0.11
644 379 0.13
645 369 0.12
646 493 0.16
647 244 0.08
648 33 0.01
649 61 0.02
650 372 0.12
651 14 0.00
652 51 0.02
653 71 0.02
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (644 bp):
TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
CATCTGAAATGTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAAATGGGAAAACGATATTGGA
AGCGTTAAAAACCCTTCAATTTTTTAAACATCAATTATATATTTTTTCCCAGTATTGTGGTAAAA
ATTTTAGAAAAAAAGTTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACTATTATT
GGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTCGGCATAAAGCCTCCTTG
AAATATCTCTATTCATTGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAGCA
TCTGAAATGTGTTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAAGCG
TTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTAAAATTT
TCAGAAAAAAATTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACAATTATAGGGC
TAAAAACGCGTTTCGGGGCCCCGCCTCAGTTTTCCATGATTTTCAGCATAAAGCGTCCT
Found at i:11056 original size:324 final size:322
Alignment explanation
Indices: 7498--11437 Score: 5333
Period size: 324 Copynumber: 12.2 Consensus size: 322
7488 ATATCTAAAA
* * * * **
7498 TGAAATATTTCTATTCATCGAACCAAATCTCAGTCACATTGGATTTAAAGATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
* * * * * *
7563 CATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATAGGAAAACTATATTGGAA
66 CATCTGAAATGTGTTTCGATTT-ATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAA
* * * * * * * *
7628 GCGTGAAAAACCCTTCAATTTTTTTTTTGCGTTAAATTATATA-TTATTCCGAGTATTGTGGCAA
130 GCGTTAAAAACCCTTCAA--TTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTAA
* * **** * * *
7692 AAATATCAGAAATTTTTTTTTCAGGTAAATTCTTA-CTCGAAATCGTGTACTAACCATCACTGTT
193 AATTTTCAGAAAAAAATTTTTCGGGTCAATTCTTAGC-CGAAATCGTGTACTAACCATCACTATT
* * * * * *
7756 AATGGGCTAAAAACGCGTTTCGGGACCCTGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCC
257 ATTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTCCATGATTTTCGGCATAAAGCCTCC
7821 T
322 T
* * * * * * * *
7822 AGAAATATCTCTATTCATCGAAACAAATCTAAGCCAAATTGGATTTAAGAATTTATTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
* * * * * *
7887 CATCTGAATTTTGTTCCGATTTAATTAGAAATAAATTCGGAAAAAATGGGAAAACGATATTAGAA
66 CATCTGAAATGTGTTTCGATTT-ATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAA
* * ** * * * *
7952 ACGTGAAAAACCCTTCAATATTTTT-T-TGTTAAATTATATATTTTTT-CGAGTATTCTGGCAAA
130 GCGTTAAAAACCCTTCAAT-TTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTAAA
* * * *
8014 AATTTCA-AAAAAAA-GTTTCGGGTCAATTCTTAGGCGAAATCGTGTACTAACCATCACTGTTAT
194 ATTTTCAGAAAAAAATTTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACTATTAT
* * * * * * * *
8077 TGGGCTAAAAACGCGTTTCGGGGCCACGACTCAGTTTTGCGTGATTTTTGGAAGAAAGCCTTCT
259 TGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTCCATGATTTTCGGCATAAAGCCTCCT
* * * *
8141 TGAAATATCTCTATTCATCGAACCAAATATCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
* * * * *
8206 CATCT-AATTTTTTTTTCGATTTAATTAGAAATAAATTCGGGAAAAAAATGGGGAAACGATATTG
66 CATCTGAA-ATGTGTTTCGATTT-ATTTGAAATAAATTC--GAAAAAAATGGGAAAACGATATTG
* * * * *
8270 GAAGTGTGAAAAACCCTTCAATTTCTTAAACATTCAATTATATATTTTTTCCAAGTATTGTGGTA
127 GAAGCGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTA
* * * *
8335 AAAATTTCATG-AAAAAATTTTTCGGGTCAATTCTTAGCCGAAATCGTGCACGTTACCATCACTG
192 AAATTTTCA-GAAAAAAATTTTTCGGGTCAATTCTTAGCCGAAATCGTGTAC-TAACCATCACTA
* * * * *
8399 TTATTGGGCTAAAAACGCATTTCGGGGCCCCGACTCAGTTTTTCATGATTTTTGGCAGAAAGCCT
255 TTATTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTCCATGATTTTCGGCATAAAGCCT
8464 CCT
320 CCT
* * * * * * **
8467 TGAAATATTTCTATTTATAGAACCAAATCTCAGCCATATTGGATTTAAAGATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
* * *
8532 CATCTG-AATTTAGTTTCGATTTAATT-AAAAAAATTCGAAAAAAATGGGAAAACGATATTGGAA
66 CATCTGAAATGT-GTTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAA
* * * * *
8595 GTGTGAAAAACCCTTCAATTTCTTAAACATTCAATTATATA-TTTTTCCAAGTATTGTGGTAAAA
130 GCGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTAAAA
* * * *
8659 ATTTCATG-AAAAAATTTTTCGGGTCAATTCTTAGACGAAATCGTGTACGTTACCATCACTGTTA
195 TTTTCA-GAAAAAAATTTTTCGGGTCAATTCTTAGCCGAAATCGTGTAC-TAACCATCACTATTA
* * * * *
8723 TTGGGCTAAAAACGCGTTTCGTGGCCACGGCTCAGTTCTT-CATGATTTTTGGCAGAAAACCTCC
258 TTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTT-TTCCATGATTTTCGGCATAAAGCCTCC
8787 T
322 T
* * * *
8788 TGAAATATCCCTATTTATTGAATCAAATCTCAGTCACATAGGATTTATGGATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
* *
8853 CATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCGAAAAAAATAGGAAAACGATATTGGAAT
66 CATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAAG
* * *
8918 CGTTAAAAACCCTTCAA-TTTTTAAACATTCAATTATATATTTTTTCCTTGTGTTGTGGTAAAAA
131 CGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGT-AAAA
*
8982 TTTT-AG-AAAAAAGTTTTCGGGTCAATTCTTAGCCGAAATCGTGTACT--CCATCACTATTATT
195 TTTTCAGAAAAAAATTTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACTATTATT
**
9043 GGGCTAAAAACGCGTTTCGGGG-CCCGGCTCAGTTTTGTATGATTTTCGGCATAAAGCCTCCT
260 GGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTCCATGATTTTCGGCATAAAGCCTCCT
* *
9105 TGAAATATCTCTATTCATTGAATCAATTCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
9170 CATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAAG
66 CATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAAG
* *
9235 CGTTAAAAACCCTTCAAATTTTTATATATTCAATTATATATTTTTTCCTAGTATTGTGGTAAAAT
131 CGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTAAAAT
* *
9300 TTTCAGAAAAAAATTTTTCGGGTCAATTCTTAGCCGGAATCGTATACTTAACCATCACTATTATT
196 TTTCAGAAAAAAATTTTTCGGGTCAATTCTTAGCCGAAATCGTGTAC-TAACCATCACTATTATT
* * * *
9365 GGGCTAAAAACGAGTTTTGGGGTCCCGGCTCAGTTTTCCATGATTTTCGGCATAAAGCGTCCT
260 GGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTCCATGATTTTCGGCATAAAGCCTCCT
* *
9428 TGAAATATCTCTATTCATTGAATCAATTCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
*
9493 CATCTGAAATGTGTTTTGATTTATTTGAAATAAATTCGAAAAAAAATGGGAAAACGATATTGGAA
66 CATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCG-AAAAAAATGGGAAAACGATATTGGAA
* * ** *
9558 GCATTAAAAACCCTTCAATTTTTTATAAACACAATTATATATTTTTTCCCAGTATTGTGGTAAAA
130 GCGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGT-AAA
* * * *
9623 ATTTT-AGAAAAAAAGTTTTCGGGTCAATTCTTAACCGAAATCGTGTACTAATCATCACTGTTAT
194 ATTTTCAGAAAAAAATTTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACTATTAT
**
9687 TGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGAATGATTTTCGGCATAAAGCCTCCT
259 TGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTCCATGATTTTCGGCATAAAGCCTCCT
* *
9751 TGAAATATCTCTATTCATTGAATCAAATCTCAGCCACATAGGAATTATGGATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
*
9816 CATCTGAAATGTGGTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAAG
66 CATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAAG
* * *
9881 CGTTAAAACCCCTTCAATTTTTTATACATTCAATTCTATATTTTTTCCTAGTATTGTGGTAAGAT
131 CGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTAAAAT
* ** * *
9946 TTTCATAAAAAAAAATTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACAATTATAG
196 TTTCAGAAAAAAATTTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACTATTATTG
* * ** ** *
10011 AGCTGAAAACGCGTTTCGGGGCCCCACCTCAGTTTTCCATGATTTTCAACATAAAGCGTCCT
261 GGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTCCATGATTTTCGGCATAAAGCCTCCT
* * *
10073 TGAAATATCTCTATTCATCGAACCAAATCTCAGCCTCATAGGATTTATGGATTTGTTTCTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
* * * * * *
10138 CATATG-ATTTTTTTTCGATTTAATTAGAAATAAATTC-AGAAAAAATGGGAAAACGATATTAGA
66 CATCTGAAATGTGTTTCGATTT-ATTTGAAATAAATTCGA-AAAAAATGGGAAAACGATATTGGA
* * *
10201 AGCGTTAAAAACCCTTCAA-TTTTTAAACATTCAATTATATATTTTTTCCTTGTGTTGTGGTAAA
129 AGCGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGT-AA
* * * *
10265 AATTTT-AGAAAAAAAGTTTTCTGGTCAATTCTTAGCCGAAATCGTGTAGTAATAATCATCACTA
193 AATTTTCAGAAAAAAATTTTTCGGGTCAATTCTTAGCCGAAATC--GT-GTACTAACCATCACTA
**
10329 TTATTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTAAATGATTTTCGGCATAAAGCCT
255 TTATTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTCCATGATTTTCGGCATAAAGCCT
10394 CCT
320 CCT
*
10397 TGAAATATCTCTATTCATTGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
*
10462 CATCTGAAATGTGTTTCGATTTATTTGAAAGAAATTCGAAAAAAAATGGGAAAACGATATTGGAA
66 CATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCG-AAAAAAATGGGAAAACGATATTGGAA
* * * *
10527 GCGTTAAAAATCCTTCAATGTTTTATACATTCAATTCTATATTTTTTCCTAGTATTGTGGTAAGA
130 GCGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTAAAA
** *
10592 TTTTCAGAAAAAAAAAAAATTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACAATT
195 TTTTCAG---AAAAAAATTTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACTATT
* * * *
10657 ATAGGGCTAAAAACGCGTTTCGGGGCCCCGCCTCAGTTTTCCATGATTTTCAGCATAAAGCGTCC
257 ATTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTCCATGATTTTCGGCATAAAGCCTCC
10722 T
322 T
*
10723 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCTCATAGGATTTATGGATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
10788 CATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCGAAAAAAAAATGGGAAAACGATATTGGA
66 CATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCG--AAAAAAATGGGAAAACGATATTGGA
*
10853 AGCGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCCAGTATTGTGGTAAA
129 AGCGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTAAA
** * *
10918 ATTTTCAGAAAAAAATTTTTCAAGTAAATTCTTAGCCGAAATCGTGTACTAACCATCACAATTAT
194 ATTTTCAGAAAAAAATTTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACTATTAT
* * * * *
10983 AGGGCTAAAAACGCGTTTCGGGGCCCCGCCTCAGTTTTCCATGATTTTCAGCATAAAGCGTTCT
259 TGGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTCCATGATTTTCGGCATAAAGCCTCCT
*
11047 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCTCATAGGATTTATGGATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
*
11112 CATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGATG
66 CATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAAG
** * * * *
11177 ATTTAAAAACCCTTCAATTTTTTATAAATTCAATTCTATA-TTTTTCTTAGTATTGTGGTAAGAT
131 CGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTAAAAT
* *
11241 TTTCAGAAAAAAA-TTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACAATTATAG
196 TTTCAGAAAAAAATTTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACTATTATTG
* * *
11305 GGCTAAAAACGCGTTTCGGGGCCCCGCCTCAGTTTTCCATGATTTTCAGCATAAAGCGTCCT
261 GGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTCCATGATTTTCGGCATAAAGCCTCCT
* ** *
11367 TGAAATATCTCTATTCATCGAATCAAATCTCAACCTTATAGGATTTATGAATTTGTTTTTACGAG
1 TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
11432 CATCTG
66 CATCTG
11438 TTCGGGTCAA
Statistics
Matches: 3295, Mismatches: 275, Indels: 96
0.90 0.08 0.03
Matches are distributed among these distances:
316 2 0.00
317 181 0.05
318 76 0.02
319 228 0.07
320 186 0.06
321 476 0.14
322 572 0.17
323 344 0.10
324 637 0.19
325 103 0.03
326 362 0.11
327 96 0.03
329 32 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (322 bp):
TGAAATATCTCTATTCATCGAATCAAATCTCAGCCACATAGGATTTATGGATTTGTTTTTACGAG
CATCTGAAATGTGTTTCGATTTATTTGAAATAAATTCGAAAAAAATGGGAAAACGATATTGGAAG
CGTTAAAAACCCTTCAATTTTTTATACATTCAATTATATATTTTTTCCTAGTATTGTGGTAAAAT
TTTCAGAAAAAAATTTTTCGGGTCAATTCTTAGCCGAAATCGTGTACTAACCATCACTATTATTG
GGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTCCATGATTTTCGGCATAAAGCCTCCT
Done.