Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007805.1 Corchorus capsularis cultivar CVL-1 contig07826, 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: 44943
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:10418 original size:46 final size:42
Alignment explanation
Indices: 10330--10412 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
10320 CAAACCTCTA
* *
10330 TTCTTTACCTAATTTCCTTCTTTGAAATTAACTCTGTGCTTT
1 TTCTTTACCTAATATCCTTCCTTGAAATTAACTCTGTGCTTT
* *
10372 TTCTTTATCTAATATCCTTCCTTGAAATTAAGTCTGTGCTT
1 TTCTTTACCTAATATCCTTCCTTGAAATTAACTCTGTGCTT
10413 GCTTTTACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.20, C:0.20, G:0.08, T:0.51
Consensus pattern (42 bp):
TTCTTTACCTAATATCCTTCCTTGAAATTAACTCTGTGCTTT
Found at i:10501 original size:37 final size:37
Alignment explanation
Indices: 10412--10830 Score: 628
Period size: 37 Copynumber: 11.4 Consensus size: 37
10402 AGTCTGTGCT
* * * *
10412 TGCTTTTACTCAATTACCTTGAATTAAG-TCTGT-GC
1 TGCTTTTACTTAATTACCCTGAATTAAGTTCTTTAAC
* * *
10447 TTGC-TTTACTCAATTACCTTGAATTAAGTCCTTTAAC
1 -TGCTTTTACTTAATTACCCTGAATTAAGTTCTTTAAC
10484 TGCTTTTACTTAATTACCCTGAATTAAGTTCTTTAAC
1 TGCTTTTACTTAATTACCCTGAATTAAGTTCTTTAAC
10521 TGCTTTTACTTAATTACCCTGAATTAAGTTCTTTAAC
1 TGCTTTTACTTAATTACCCTGAATTAAGTTCTTTAAC
10558 TGCTTTTACTTAATTACCCTGAATTAAGTTCTTTAAC
1 TGCTTTTACTTAATTACCCTGAATTAAGTTCTTTAAC
*
10595 TGCTTTGACTTAATTACCCTGAATTAAGTTCTTTAAC
1 TGCTTTTACTTAATTACCCTGAATTAAGTTCTTTAAC
**
10632 TATTTTTACTTAATTACCCTGAATTAAGTTCTTTAAC
1 TGCTTTTACTTAATTACCCTGAATTAAGTTCTTTAAC
* *
10669 TACTTTTACTTAATTACCCTGAACTAAGTTCTTTAAC
1 TGCTTTTACTTAATTACCCTGAATTAAGTTCTTTAAC
*
10706 TGCTTTTACTTAATTACCCTGAATTAGGTTCTTTAAC
1 TGCTTTTACTTAATTACCCTGAATTAAGTTCTTTAAC
* * * *
10743 TGATATTAGTTAATTATCCTGAATTAAGTTCTTTAAC
1 TGCTTTTACTTAATTACCCTGAATTAAGTTCTTTAAC
* * *
10780 TACTTTTTCTTAATTACCCTTAATTAAGTTCTTTAAC
1 TGCTTTTACTTAATTACCCTGAATTAAGTTCTTTAAC
10817 TGCTTTTACTTAAT
1 TGCTTTTACTTAAT
10831 CATCTTGAGT
Statistics
Matches: 351, Mismatches: 29, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
35 24 0.07
36 9 0.03
37 318 0.91
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.46
Consensus pattern (37 bp):
TGCTTTTACTTAATTACCCTGAATTAAGTTCTTTAAC
Found at i:18500 original size:13 final size:14
Alignment explanation
Indices: 18476--18505 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
18466 GAATTAAAAT
18476 TAAATCTAACTAAG
1 TAAATCTAACTAAG
18490 TAAAT-TAACTAAG
1 TAAATCTAACTAAG
18503 TAA
1 TAA
18506 GCAATCAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (14 bp):
TAAATCTAACTAAG
Found at i:19785 original size:19 final size:18
Alignment explanation
Indices: 19752--19787 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19742 TTGAAATAAT
19752 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
19770 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
19788 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:23644 original size:29 final size:26
Alignment explanation
Indices: 23612--23680 Score: 68
Period size: 29 Copynumber: 2.5 Consensus size: 26
23602 AAGGAGAGGG
23612 AAAGAAAAAAAATGAAGAA-AAGAATTGAA
1 AAAGAAAAAAAA--AAGAAGAAG--TTGAA
23641 AAAGAAAAGGAAAAAAGAAGAAGTTGAA
1 AAAGAAAA--AAAAAAGAAGAAGTTGAA
*
23669 AAAGTAAAAAAA
1 AAAGAAAAAAAA
23681 GGAGCAAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
26 4 0.11
28 12 0.33
29 13 0.36
30 3 0.08
31 4 0.11
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (26 bp):
AAAGAAAAAAAAAAGAAGAAGTTGAA
Found at i:25015 original size:34 final size:34
Alignment explanation
Indices: 24948--25220 Score: 368
Period size: 34 Copynumber: 7.9 Consensus size: 34
24938 GAGTCATGTA
*
24948 CAGTTGACCCAGGGCGGTCGTCTTTATTCAGTTTATT
1 CAGTTGACCCAGGGC-G--GTCTTTCTTCAGTTTATT
* * *
24985 CAGTTGACCTAGAGCGGTCTTTCTTAAGTTTATTT
1 CAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA-TT
* * * *
25020 TAGTTTACCCAGGGCAGTCTTTCTTAAGTTTATTT
1 CAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA-TT
25055 CAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATT
1 CAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATT
* *
25089 CAGTTGACCTAGGATC-GTCTTTCTTCAGTTTATT
1 CAGTTGACCCAGG-GCGGTCTTTCTTCAGTTTATT
*
25123 CAGTTGACCCAGGGCGGTCTTTCATCAGTTTATT
1 CAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATT
25157 CAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATT
1 CAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATT
* *
25191 CAGTTGACCCAGGGCGGTATTTATTCAGTT
1 CAGTTGACCCAGGGCGGTCTTTCTTCAGTT
25221 GATTTCCAAA
Statistics
Matches: 212, Mismatches: 21, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
33 1 0.00
34 136 0.64
35 61 0.29
36 1 0.00
37 13 0.06
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.40
Consensus pattern (34 bp):
CAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATT
Found at i:25290 original size:35 final size:35
Alignment explanation
Indices: 25244--25456 Score: 272
Period size: 35 Copynumber: 6.1 Consensus size: 35
25234 CCCAATGTGG
*
25244 TCATTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCA-ACGATCAGAGTTGATC
* *
25279 TCATTTCAAGAAG-TTTCTAAAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTC-AACGATCAGAGTTGATC
*
25314 TCATTTCAAGAAGTTTCCAACGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAACGATCAGAGTTGATC
* *
25349 TGA-TTCAAAAAAGTTTTCGAA-GATCAGAGTTGATC
1 TCATTTC-AAGAAGTTTTC-AACGATCAGAGTTGATC
* *
25384 TCATTCCAAGAAGTTTTCAACGATCGGAGTTGATC
1 TCATTTCAAGAAGTTTTCAACGATCAGAGTTGATC
* *
25419 TCATTTTAAGAAGTTTTCAATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAACGATCAGAGTTGATC
25454 TCA
1 TCA
25457 AATTGATCTG
Statistics
Matches: 157, Mismatches: 14, Indels: 14
0.85 0.08 0.08
Matches are distributed among these distances:
34 10 0.06
35 140 0.89
36 7 0.04
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (35 bp):
TCATTTCAAGAAGTTTTCAACGATCAGAGTTGATC
Found at i:25519 original size:35 final size:35
Alignment explanation
Indices: 25473--25545 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
25463 TCTGATGTGG
25473 TCATTCCAAGAAGTTTTCAACGATCAGAGTTGATC
1 TCATTCCAAGAAGTTTTCAACGATCAGAGTTGATC
* *
25508 TCATTTCAAGAAGTTTTCAATGATCAGAGTTGATC
1 TCATTCCAAGAAGTTTTCAACGATCAGAGTTGATC
25543 TCA
1 TCA
25546 GATTGATCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (35 bp):
TCATTCCAAGAAGTTTTCAACGATCAGAGTTGATC
Found at i:25535 original size:89 final size:89
Alignment explanation
Indices: 25384--25597 Score: 340
Period size: 89 Copynumber: 2.4 Consensus size: 89
25374 AGAGTTGATC
* *
25384 TCATTCCAAGAAGTTTTCAACGATCGGAGTTGATCTCATTTTAAGAAGTTTTCAATGATCAGAGT
1 TCATTCCAAGAAGTTTTCAACGATCAGAGTTGATCTCATTTCAAGAAGTTTTCAATGATCAGAGT
*
25449 TGATCTCAAATTGATCTGATGTGG
66 TGATCTCAAATTGATCCGATGTGG
25473 TCATTCCAAGAAGTTTTCAACGATCAGAGTTGATCTCATTTCAAGAAGTTTTCAATGATCAGAGT
1 TCATTCCAAGAAGTTTTCAACGATCAGAGTTGATCTCATTTCAAGAAGTTTTCAATGATCAGAGT
* *
25538 TGATCTCAGATTGATCCGTTGTGG
66 TGATCTCAAATTGATCCGATGTGG
* ** *
25562 TCATTTCAAGAAGTTTTGGA-GTTCAGAGTTGATCTC
1 TCATTCCAAGAAGTTTTCAACGATCAGAGTTGATCTC
25598 CAATTGATCC
Statistics
Matches: 116, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 15 0.13
89 101 0.87
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (89 bp):
TCATTCCAAGAAGTTTTCAACGATCAGAGTTGATCTCATTTCAAGAAGTTTTCAATGATCAGAGT
TGATCTCAAATTGATCCGATGTGG
Found at i:25660 original size:54 final size:54
Alignment explanation
Indices: 25508--25890 Score: 450
Period size: 54 Copynumber: 7.1 Consensus size: 54
25498 AGAGTTGATC
** * *
25508 TCATTTCAAGAAGTTTTCAATGATCAGAGTTGATCT-CAGATTGATCCGTTGTGG
1 TCATTTCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCCA-ATTGATCCGGTGTGG
* * * * *
25562 TCATTTCAAGAAGTTTT-GGAGTTCAGAGTTGATCTCCAATTGATCCAGTGCGA
1 TCATTTCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGTGG
* **
25615 TCATTTCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCGAATTGATCTAGTGTGG
1 TCATTTCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGTGG
* * * *
25669 TCATTCCAAGAAG-TTTCGGTGGTCAGAGTTGACCCCCAATTGATCTGGTGTGG
1 TCATTTCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGTGG
* * * * * * ** *
25722 TCGTCTCAAGAAATTTTCAGTGGTCATAGTTGATCTCGAA-TGGGCCGGTGCGG
1 TCATTTCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGTGG
* *
25775 TCATTTAAAGAAGTTTTCGGTGGTCAGAGTTGATCTCCAATTGATACGGTGTGG
1 TCATTTCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGTGG
* * * *
25829 TCGTCTCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCGAATTGATCCGGTGCGG
1 TCATTTCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGTGG
25883 TCATTTCA
1 TCATTTCA
25891 GAAAGATTTC
Statistics
Matches: 274, Mismatches: 51, Indels: 8
0.82 0.15 0.02
Matches are distributed among these distances:
53 129 0.47
54 145 0.53
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.34
Consensus pattern (54 bp):
TCATTTCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGTGG
Found at i:25695 original size:107 final size:106
Alignment explanation
Indices: 25508--25890 Score: 444
Period size: 107 Copynumber: 3.6 Consensus size: 106
25498 AGAGTTGATC
* * * *
25508 TCATTTCAAGAAGTTTTCAATGATCAGAGTTGATCTC-AGATTGATCCGTTGTGGTCATTTCAAG
1 TCATCTCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCGA-ATTGATCAG-TGTGGTCATTTCAAG
* * * * * *
25572 AAGTTTTGGAGTTCAGAGTTGATCTCCAATTGATCCAGTGCGA
64 AAGTTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGTGG
* * *
25615 TCATTTCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCGAATTGATCTAGTGTGGTCATTCCAAGA
1 TCATCTCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCGAATTGATC-AGTGTGGTCATTTCAAGA
* * *
25680 AGTTTCGGTGGTCAGAGTTGACCCCCAATTGATCTGGTGTGG
65 AGTTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGTGG
* * * * ** * * *
25722 TCGTCTCAAGAAATTTTCAGTGGTCATAGTTGATCTCGAATGGGCCGGTGCGGTCATTTAAAGAA
1 TCATCTCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCGAATTGATCAGTGTGGTCATTTCAAGAA
*
25787 GTTTTCGGTGGTCAGAGTTGATCTCCAATTGATACGGTGTGG
66 G-TTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGTGG
* * * *
25829 TCGTCTCAAGAAGTTTTCGGTGGTCAGAGTTGATCTCGAATTGATCCGGTGCGGTCATTTCA
1 TCATCTCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCGAATTGAT-CAGTGTGGTCATTTCA
25891 GAAAGATTTC
Statistics
Matches: 235, Mismatches: 37, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
106 16 0.07
107 202 0.86
108 17 0.07
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.34
Consensus pattern (106 bp):
TCATCTCAAGAAGTTTTCAGTGGTCAGAGTTGATCTCGAATTGATCAGTGTGGTCATTTCAAGAA
GTTTCGGTGGTCAGAGTTGATCTCCAATTGATCCGGTGTGG
Found at i:27372 original size:12 final size:12
Alignment explanation
Indices: 27355--27636 Score: 76
Period size: 12 Copynumber: 23.3 Consensus size: 12
27345 TAAATTATTT
27355 TATTTATTTATC
1 TATTTATTTATC
27367 TATTTATTATTATC
1 TATTTA-T-TTATC
* *
27381 TATCTATCTATC
1 TATTTATTTATC
*
27393 TACTTAGTTT-T-
1 TATTTA-TTTATC
27404 T-TTGT-TTTATC
1 TATT-TATTTATC
*
27415 TATTTA-CTAT-
1 TATTTATTTATC
27425 TCATTT-TCTTATC
1 T-ATTTAT-TTATC
*
27438 TATTTGTAATTAT-
1 TA-TT-TATTTATC
27451 TATTTATTATTATC
1 TATTTA-T-TTATC
*
27465 TATTTAGTACTAT-
1 TATTTA-T-TTATC
*
27478 TATCTATTTAATAC
1 TATTTATTT-AT-C
27492 TA-TTATTTATC
1 TATTTATTTATC
*
27503 TATCT-TTTA--
1 TATTTATTTATC
*
27512 T-TTTAGTATATCC
1 TATTTA-TTTAT-C
* *
27525 T-TCTAATTATC
1 TATTTATTTATC
* **
27536 TATTAAGCTAT-
1 TATTTATTTATC
*
27547 TATTTATTTATT
1 TATTTATTTATC
* *
27559 TATATATATATATA
1 TAT-T-TATTTATC
*
27573 TATTTGTTTA-C
1 TATTTATTTATC
*
27584 ATACTTATTTATC
1 -TATTTATTTATC
* *
27597 TATTTGTTTATA
1 TATTTATTTATC
27609 TATTTATTTATC
1 TATTTATTTATC
*
27621 TTTTTATTTATC
1 TATTTATTTATC
27633 TATT
1 TATT
27637 GTTTTTTTAT
Statistics
Matches: 195, Mismatches: 42, Indels: 66
0.64 0.14 0.22
Matches are distributed among these distances:
8 2 0.01
9 4 0.02
10 6 0.03
11 31 0.16
12 85 0.44
13 30 0.15
14 37 0.19
ACGTcount: A:0.27, C:0.10, G:0.03, T:0.61
Consensus pattern (12 bp):
TATTTATTTATC
Found at i:27478 original size:17 final size:16
Alignment explanation
Indices: 27433--27497 Score: 68
Period size: 17 Copynumber: 4.2 Consensus size: 16
27423 ATTCATTTTC
27433 TTATCTATTT-GTA-A
1 TTATCTATTTAGTATA
27447 TTAT-TATTTA-T-TA
1 TTATCTATTTAGTATA
27460 TTATCTATTTAGTACTA
1 TTATCTATTTAGTA-TA
*
27477 TTATCTATTTAATACTA
1 TTATCTATTTAGTA-TA
27494 TTAT
1 TTAT
27498 TTATCTATCT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
13 11 0.25
14 10 0.23
15 1 0.02
17 22 0.50
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (16 bp):
TTATCTATTTAGTATA
Found at i:27555 original size:4 final size:4
Alignment explanation
Indices: 27546--27649 Score: 61
Period size: 4 Copynumber: 25.8 Consensus size: 4
27536 TATTAAGCTA
* * * * * *
27546 TTAT TTAT TTAT TTAT ATATAT ATAT ATAT TTGT TTAC ATAC TTAT TTAT
1 TTAT TTAT TTAT TTAT -T-TAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * *
27596 CTAT TTGT TTAT ATAT TTAT TTAT CTT-T TTAT TTAT CTAT TGT-T TT-T
1 TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT T-TAT TTAT
27643 TTAT TTA
1 TTAT TTA
27650 CATAGTAGTT
Statistics
Matches: 78, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
3 6 0.08
4 65 0.83
5 4 0.05
6 3 0.04
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (4 bp):
TTAT
Found at i:27631 original size:24 final size:24
Alignment explanation
Indices: 27546--27636 Score: 87
Period size: 24 Copynumber: 3.9 Consensus size: 24
27536 TATTAAGCTA
*
27546 TTATTTATTTATTTATATA--TAT
1 TTATCTATTTATTTATATATTTAT
* * * * *
27568 ATATATATTTGTTTACATACTTAT
1 TTATCTATTTATTTATATATTTAT
*
27592 TTATCTATTTGTTTATATATTTAT
1 TTATCTATTTATTTATATATTTAT
* *
27616 TTATCTTTTTATTTATCTATT
1 TTATCTATTTATTTATATATT
27637 GTTTTTTTAT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
22 15 0.27
24 41 0.73
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.65
Consensus pattern (24 bp):
TTATCTATTTATTTATATATTTAT
Found at i:41587 original size:13 final size:13
Alignment explanation
Indices: 41569--41593 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41559 AAAAATGTAT
41569 AAGTATAGTTTAG
1 AAGTATAGTTTAG
41582 AAGTATAGTTTA
1 AAGTATAGTTTA
41594 AATGTGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (13 bp):
AAGTATAGTTTAG
Found at i:41658 original size:31 final size:31
Alignment explanation
Indices: 41623--41714 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
41613 TTTTTAGCGT
*
41623 GGTTAATACTATAAATCTTTGATTTTAATTG
1 GGTTAATACTATAAATCTTTAATTTTAATTG
* *
41654 GGTTAATACTATAAAAT-TTTCATTTT-AGTG
1 GGTTAATACTAT-AAATCTTTAATTTTAATTG
* * *
41684 GGTCAATACTGTAAAACTTTAATTGTTAATT
1 GGTTAATACTATAAATCTTTAATT-TTAATT
41715 TTCCCCTTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
29 3 0.06
30 19 0.38
31 22 0.44
32 6 0.12
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.46
Consensus pattern (31 bp):
GGTTAATACTATAAATCTTTAATTTTAATTG
Found at i:41692 original size:30 final size:32
Alignment explanation
Indices: 41627--41712 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 32
41617 TAGCGTGGTT
* * *
41627 AATACTAT-AAATCTTTGATTTTAATTGGGTT
1 AATACTATAAAATCTTTCATTTTAAGTGGGTC
41658 AATACTATAAAAT-TTTCATTTT-AGTGGGTC
1 AATACTATAAAATCTTTCATTTTAAGTGGGTC
* *
41688 AATACTGTAAAA-CTTTAATTGTTAA
1 AATACTATAAAATCTTTCATT-TTAA
41713 TTTTCCCCTT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
30 23 0.50
31 18 0.39
32 5 0.11
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (32 bp):
AATACTATAAAATCTTTCATTTTAAGTGGGTC
Done.