Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007917.1 Corchorus capsularis cultivar CVL-1 contig07938, 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: 17843
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Found at i:5562 original size:19 final size:19
Alignment explanation
Indices: 5540--5586 Score: 64
Period size: 17 Copynumber: 2.6 Consensus size: 19
5530 AAAAGGAAGG
5540 ATAAAAGGAAAATGAA-AAA
1 ATAAAA-GAAAATGAAGAAA
5559 ATAAAA-AAAATGAAGAAA
1 ATAAAAGAAAATGAAGAAA
5577 A-AAAAGAAAA
1 ATAAAAGAAAA
5587 AGAGAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 12 0.46
18 8 0.31
19 6 0.23
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.09
Consensus pattern (19 bp):
ATAAAAGAAAATGAAGAAA
Found at i:5570 original size:17 final size:18
Alignment explanation
Indices: 5542--5595 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
5532 AAGGAAGGAT
*
5542 AAAAGGAAAATGAA-AAA
1 AAAAAGAAAATGAAGAAA
5559 ATAAAA-AAAATGAAGAAA
1 A-AAAAGAAAATGAAGAAA
*
5577 AAAAAGAAAAAG-AGAAA
1 AAAAAGAAAATGAAGAAA
5594 AA
1 AA
5596 GCAACGATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 20 0.62
18 12 0.38
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.06
Consensus pattern (18 bp):
AAAAAGAAAATGAAGAAA
Found at i:5586 original size:35 final size:36
Alignment explanation
Indices: 5528--5595 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 36
5518 GAAAAAAGTG
* * * *
5528 AAAAAAGGAAGGATAAAAGGAAAATGA-AAAAATAA
1 AAAAAAGGAAGAAAAAAAAGAAAAAGAGAAAAATAA
*
5563 AAAAAATGAAGAAAAAAAAGAAAAAGAGAAAAA
1 AAAAAAGGAAGAAAAAAAAGAAAAAGAGAAAAA
5596 GCAACGATGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 22 0.81
36 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (36 bp):
AAAAAAGGAAGAAAAAAAAGAAAAAGAGAAAAATAA
Found at i:5659 original size:25 final size:25
Alignment explanation
Indices: 5625--5684 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
5615 AGAGTCATGA
* *
5625 TTTTCAAAAGGTTTTGCTAAAATGG
1 TTTTCAAAAGATTTTGATAAAATGG
5650 TTTTCAAAAGATTTTGATAAAATGG
1 TTTTCAAAAGATTTTGATAAAATGG
5675 TTTTCCAAAA
1 TTTT-CAAAA
5685 ATGATTTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 27 0.84
26 5 0.16
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (25 bp):
TTTTCAAAAGATTTTGATAAAATGG
Found at i:6041 original size:20 final size:20
Alignment explanation
Indices: 6018--6060 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
6008 ATGTAAAAAA
6018 AAAAAAGAAGAAAA-AAAGTG
1 AAAAAAGAA-AAAAGAAAGTG
**
6038 AAAATTGAAAAAAGAAAGTG
1 AAAAAAGAAAAAAGAAAGTG
6058 AAA
1 AAA
6061 GGAAAGGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (20 bp):
AAAAAAGAAAAAAGAAAGTG
Found at i:14057 original size:33 final size:33
Alignment explanation
Indices: 13939--14045 Score: 180
Period size: 33 Copynumber: 3.2 Consensus size: 33
13929 TTCTTTTCAC
*
13939 CCAAAACAAAATTATTTGCAATGCTATGATCAA
1 CCAAAACAAAATTATTTTCAATGCTATGATCAA
13972 CCAAAA-AAGAATTATTTTCAATGCTATGATCAA
1 CCAAAACAA-AATTATTTTCAATGCTATGATCAA
*
14005 CCAAAACAAAATTATTTTCAATGTTATGATCAA
1 CCAAAACAAAATTATTTTCAATGCTATGATCAA
14038 CCAAAACA
1 CCAAAACA
14046 GATTTGTTTT
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.03
33 66 0.94
34 2 0.03
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (33 bp):
CCAAAACAAAATTATTTTCAATGCTATGATCAA
Found at i:14075 original size:66 final size:66
Alignment explanation
Indices: 13939--14076 Score: 170
Period size: 66 Copynumber: 2.1 Consensus size: 66
13929 TTCTTTTCAC
* * *
13939 CCAAAACAAAATTATTTGCAATGCTATGATCAACCAAAAAAGAATTATTTTCAATGCTATGATCA
1 CCAAAACAAAATTATTTGCAATGCTATGATCAACCAAAAAAGAATTATTTTCAATACAATGAGCA
14004 A
66 A
* * * * * *
14005 CCAAAACAAAATTATTTTCAATGTTATGATCAACCAAAACAGATTTGTTTTC-ATCACAATTAGC
1 CCAAAACAAAATTATTTGCAATGCTATGATCAACCAAAAAAGAATTATTTTCAAT-ACAATGAGC
*
14069 AT
65 AA
14071 CCAAAA
1 CCAAAA
14077 TAGATTTAGT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
65 2 0.03
66 59 0.97
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (66 bp):
CCAAAACAAAATTATTTGCAATGCTATGATCAACCAAAAAAGAATTATTTTCAATACAATGAGCA
A
Found at i:14109 original size:33 final size:33
Alignment explanation
Indices: 14072--14168 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 33
14062 AATTAGCATC
**
14072 CAAAATAGATTTAGTATCATCACAAACAACACT
1 CAAAATAGATTTAGTATCATTGCAAACAACACT
* *
14105 CAAAACAGATTTAGTGTCATTGCAAACAACACT
1 CAAAATAGATTTAGTATCATTGCAAACAACACT
* *
14138 CAAATTAGGTTTAGTATCATTGCAAACAACA
1 CAAAATAGATTTAGTATCATTGCAAACAACA
14169 TCTAAAACAC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.26
Consensus pattern (33 bp):
CAAAATAGATTTAGTATCATTGCAAACAACACT
Found at i:17357 original size:2 final size:2
Alignment explanation
Indices: 17350--17390 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
17340 CTTGTTTCTT
*
17350 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17391 TGTTAATTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Done.