Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011707.1 Corchorus capsularis cultivar CVL-1 contig11728, 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: 44593
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--31 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1 AT AT 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 AT AT A
32 CTAGTTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3142 original size:30 final size:25
Alignment explanation
Indices: 3086--3135 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3076 TAGTCAACTG
3086 TTTGTTTAAAATAAAAGATTATATA
1 TTTGTTTAAAATAAAAGATTATATA
3111 TTTGTTTAAAATAAAAGATTATATA
1 TTTGTTTAAAATAAAAGATTATATA
3136 ATATATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (25 bp):
TTTGTTTAAAATAAAAGATTATATA
Found at i:3144 original size:25 final size:25
Alignment explanation
Indices: 3091--3144 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
3081 AACTGTTTGT
* *
3091 TTAAAATAAAAGATTATATATTTGT
1 TTAAAATAAAAGATTATATATATGA
3116 TTAAAATAAAAGATTATATAATAT-A
1 TTAAAATAAAAGATTATAT-ATATGA
3141 TTAA
1 TTAA
3145 TTAATGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 23 0.88
26 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.41
Consensus pattern (25 bp):
TTAAAATAAAAGATTATATATATGA
Found at i:11375 original size:6 final size:6
Alignment explanation
Indices: 11364--11396 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
11354 ATTGCCATCA
11364 TGGTTC TGGTTC TGGTTC TGGTTC TGGTTC TGG
1 TGGTTC TGGTTC TGGTTC TGGTTC TGGTTC TGG
11397 ACACACTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.36, T:0.48
Consensus pattern (6 bp):
TGGTTC
Found at i:11807 original size:2 final size:2
Alignment explanation
Indices: 11800--11826 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11790 AAAAACCATT
11800 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
11827 TTGGATAAGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16599 original size:102 final size:101
Alignment explanation
Indices: 16441--16746 Score: 382
Period size: 102 Copynumber: 3.0 Consensus size: 101
16431 CGGATTTTTC
* * * *
16441 TGTAGTAATTTCCGTTGGAACAAAATT-TTTTTGGCGCAAAATATTTGGGCTAGCGGGAATTCGA
1 TGTAGTAATTTCCGTT-GCA-AAAATTAATTTTGGCGCAAAATATTTAGG--AGCGGGAATTCAA
* * *
16505 ATTTTAATTTATCACGAAAGTTAAAATCGTTGCAAAATTT
62 ATTTTAATTTGTCACGAAAATTAAATTCGTTGCAAAATTT
*
16545 TGTAGTAATTTCCGTTGCAAAAATTAATTTTGGCGCAAAATATTTAAGGAGCGGGAATTCAAAAT
1 TGTAGTAATTTCCGTTGCAAAAATTAATTTTGGCGCAAAATATTT-AGGAGCGGGAATTCAAATT
* * *
16610 TTAATTTGTTATGAAAACTAAATTCGTTGCAAAATTT
65 TTAATTTGTCACGAAAATTAAATTCGTTGCAAAATTT
* * *
16647 CGTAATAATTT-CGTTGCAAAAATTAATTTTGGCGCAAAATTTTTGAGCGAGCGGGAATTCAAAT
1 TGTAGTAATTTCCGTTGCAAAAATTAATTTTGGCGCAAAATATTT-AG-GAGCGGGAATTCAAAT
* * *
16711 TTTAATTTGCCACGAAAATTAATTTCGTGGCAAAAT
64 TTTAATTTGTCACGAAAATTAAATTCGTTGCAAAAT
16747 CTGTAGCAAA
Statistics
Matches: 177, Mismatches: 22, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
101 34 0.19
102 105 0.59
103 20 0.11
104 18 0.10
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (101 bp):
TGTAGTAATTTCCGTTGCAAAAATTAATTTTGGCGCAAAATATTTAGGAGCGGGAATTCAAATTT
TAATTTGTCACGAAAATTAAATTCGTTGCAAAATTT
Found at i:24383 original size:19 final size:18
Alignment explanation
Indices: 24359--24394 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
24349 AAAAAAATTA
24359 AAAATAAAAAATGTATTTT
1 AAAATAAAAAAT-TATTTT
*
24378 AAAATATAAAATTATTT
1 AAAATAAAAAATTATTT
24395 ATTTAAAATA
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:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
AAAATAAAAAATTATTTT
Found at i:25194 original size:26 final size:25
Alignment explanation
Indices: 25143--25221 Score: 63
Period size: 27 Copynumber: 3.1 Consensus size: 25
25133 AGGATACAAC
* * *
25143 TAATA-AAAAATATTTTTTATATTA
1 TAATATAAAAATATTATTTAAAATA
25167 TAATATAAAAATATTCATTTAAAATA
1 TAATATAAAAATATT-ATTTAAAATA
* *
25193 TAGATATTAATACT-TTAATTTAAAATA
1 TA-ATA-TAAAAATATT-ATTTAAAATA
25220 TA
1 TA
25222 TGTAAATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
24 5 0.11
25 9 0.20
26 9 0.20
27 17 0.38
28 5 0.11
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (25 bp):
TAATATAAAAATATTATTTAAAATA
Found at i:26347 original size:75 final size:75
Alignment explanation
Indices: 26222--26375 Score: 281
Period size: 75 Copynumber: 2.1 Consensus size: 75
26212 TGGGTTGTTA
26222 TTTTCCGGCGGTGGTTAGGGTATTGGCATGGTGGCGAAGATTGATAACATGGTGGCTAACGGTGA
1 TTTTCCGGCGGTGGTTAGGGTATTGGCATGGTGGCGAAGATTGATAACATGGTGGCTAACGGTGA
*
26287 TGATGCTGAG
66 TGATGCTAAG
* *
26297 TTTTCCGGCGGTGGTTAGGGTATTGGCATGGTGGCGAAGGTTGATGACATGGTGGCTAACGGTGA
1 TTTTCCGGCGGTGGTTAGGGTATTGGCATGGTGGCGAAGATTGATAACATGGTGGCTAACGGTGA
26362 TGATGCTAAG
66 TGATGCTAAG
26372 TTTT
1 TTTT
26376 GGAGAAGATC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.19, C:0.12, G:0.38, T:0.31
Consensus pattern (75 bp):
TTTTCCGGCGGTGGTTAGGGTATTGGCATGGTGGCGAAGATTGATAACATGGTGGCTAACGGTGA
TGATGCTAAG
Found at i:26512 original size:21 final size:21
Alignment explanation
Indices: 26488--26534 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
26478 AAAAATCTTT
*
26488 ATTTTATATAAATA-ATTTTAA
1 ATTTTA-AAAAATACATTTTAA
*
26509 ATTTTAAAAAATACATTTTTA
1 ATTTTAAAAAATACATTTTAA
26530 ATTTT
1 ATTTT
26535 TTATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTTAAAAAATACATTTTAA
Found at i:26915 original size:30 final size:30
Alignment explanation
Indices: 26879--26939 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
26869 ATACAAACAC
26879 CAAAATCAACATTTTGTAATACAAGGACCT
1 CAAAATCAACATTTTGTAATACAAGGACCT
26909 CAAAATCAACATTTTGTAATACAAGGACCT
1 CAAAATCAACATTTTGTAATACAAGGACCT
26939 C
1 C
26940 CCAAGTTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (30 bp):
CAAAATCAACATTTTGTAATACAAGGACCT
Found at i:27448 original size:2 final size:2
Alignment explanation
Indices: 27436--27473 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
27426 AACCATTACC
27436 AT AT A- AT AT AT 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 AT AT AT AT AT AT A
27474 GATTAATTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:32120 original size:30 final size:30
Alignment explanation
Indices: 32062--32122 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
32052 GCAAAAAGTG
* *
32062 AAGAAGAGTAGTAAAATTTTACCAAAAAAA
1 AAGAAGAGTAGTAAAATGTTAACAAAAAAA
*
32092 AAGAAGAGTAGTAAAA-GTTAACATAAAAA
1 AAGAAGAGTAGTAAAATGTTAACAAAAAAA
32121 AA
1 AA
32123 TAATGAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.62, C:0.05, G:0.15, T:0.18
Consensus pattern (30 bp):
AAGAAGAGTAGTAAAATGTTAACAAAAAAA
Found at i:32506 original size:5 final size:6
Alignment explanation
Indices: 32484--32514 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
32474 CTTGCCTCAA
32484 AAAAAGT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAA-T AAAAAT AAAAAT AAAAAT AAAAAT
32515 TCCTTTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:36662 original size:37 final size:37
Alignment explanation
Indices: 36616--36690 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
36606 TTTAATCCTT
* * * *
36616 CTTTTGTAAAGAGTATAGCTAATATTTTGGCTGTGTG
1 CTTTAGTAAAGAGTATAACTAATATCTTGGCTGCGTG
*
36653 CTTTAGTAAAGAGTATAATTAATATCTTGGCTGCGTG
1 CTTTAGTAAAGAGTATAACTAATATCTTGGCTGCGTG
36690 C
1 C
36691 AGTAGCCAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.40
Consensus pattern (37 bp):
CTTTAGTAAAGAGTATAACTAATATCTTGGCTGCGTG
Found at i:39272 original size:40 final size:40
Alignment explanation
Indices: 39228--39304 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
39218 GGGTAAGTCC
39228 CCCAAATTTGAGATTTTATTGGGATAGAGTTTTAGAATTA
1 CCCAAATTTGAGATTTTATTGGGATAGAGTTTTAGAATTA
39268 CCCAAATTTGAGATTTTATTGGGATAGAGTTTTAGAA
1 CCCAAATTTGAGATTTTATTGGGATAGAGTTTTAGAA
39305 AATTGATAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (40 bp):
CCCAAATTTGAGATTTTATTGGGATAGAGTTTTAGAATTA
Found at i:40623 original size:145 final size:145
Alignment explanation
Indices: 40468--40758 Score: 582
Period size: 145 Copynumber: 2.0 Consensus size: 145
40458 CTCATGTCCC
40468 TTTTTTTTTAATTATGCAAAATGACAATTTTGTTTATAAATTATATATGACCATGAACAATAGTT
1 TTTTTTTTTAATTATGCAAAATGACAATTTTGTTTATAAATTATATATGACCATGAACAATAGTT
40533 TGAATTATTATAAAGGATTCAGATTCTGCAATGTTGCCGGGAACTTTTACACTACAATTGGCGAT
66 TGAATTATTATAAAGGATTCAGATTCTGCAATGTTGCCGGGAACTTTTACACTACAATTGGCGAT
40598 GTGAGTTGGTTCATA
131 GTGAGTTGGTTCATA
40613 TTTTTTTTTAATTATGCAAAATGACAATTTTGTTTATAAATTATATATGACCATGAACAATAGTT
1 TTTTTTTTTAATTATGCAAAATGACAATTTTGTTTATAAATTATATATGACCATGAACAATAGTT
40678 TGAATTATTATAAAGGATTCAGATTCTGCAATGTTGCCGGGAACTTTTACACTACAATTGGCGAT
66 TGAATTATTATAAAGGATTCAGATTCTGCAATGTTGCCGGGAACTTTTACACTACAATTGGCGAT
40743 GTGAGTTGGTTCATA
131 GTGAGTTGGTTCATA
40758 T
1 T
40759 ACCTTTCCTG
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 146 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (145 bp):
TTTTTTTTTAATTATGCAAAATGACAATTTTGTTTATAAATTATATATGACCATGAACAATAGTT
TGAATTATTATAAAGGATTCAGATTCTGCAATGTTGCCGGGAACTTTTACACTACAATTGGCGAT
GTGAGTTGGTTCATA
Found at i:42648 original size:190 final size:189
Alignment explanation
Indices: 42317--42701 Score: 693
Period size: 190 Copynumber: 2.0 Consensus size: 189
42307 TGAAATATCT
*
42317 AAAATACCATTTTTAATTTTAAATATTATAAATAGCTTTTAAGGTTTAATATGTAATTTTATTTA
1 AAAAAACCATTTTTAATTTTAAATATTATAAATAGCTTTTAAGGTTTAATATGTAATTTTATTTA
42382 TCAATTAAATTAAGATTAATTATCAAGTGCCCCTCTCCAAATATTCTTCTAAGATCTACTCGGTT
66 TCAATTAAATTAAGATTAATTATCAAGTGCCCCTCTCCAAATATTCTTCTAAGATCTACTCGGTT
*
42447 AAAGCTTTATTTCTCTTTCCATCTCTTTTTCACGTTTTCTTCTCT-TTTTTTTTCTTAA
131 AAAGATTTATTTCTCTTTCCATCTCTTTTTCACGTTTTCTTCTCTCTTTTTTTTCTTAA
42505 AAAAAACC-TTTTTAATTTTAAATATTATTAAATAGCTTTTAAAGGTTTAATATGTAATTTTATT
1 AAAAAACCATTTTTAATTTTAAATATTA-TAAATAGCTTTT-AAGGTTTAATATGTAATTTTATT
* *
42569 TATCAATTAAATTTAAGATTATTTATCAAGTGCCCCTCTCCAAATATTCTTCTAAGATTTACTCG
64 TATCAATTAAA-TTAAGATTAATTATCAAGTGCCCCTCTCCAAATATTCTTCTAAGATCTACTCG
42634 GTTAAAGATTTATTTCTCTTTCCATCTCTTTTTCACGTTTTCTTCTCTCTTTTTTTTCTTAA
128 GTTAAAGATTTATTTCTCTTTCCATCTCTTTTTCACGTTTTCTTCTCTCTTTTTTTTCTTAA
42696 AAAAAA
1 AAAAAA
42702 ATTCTCTCAA
Statistics
Matches: 189, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
187 19 0.10
188 19 0.10
189 34 0.18
190 98 0.52
191 19 0.10
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.48
Consensus pattern (189 bp):
AAAAAACCATTTTTAATTTTAAATATTATAAATAGCTTTTAAGGTTTAATATGTAATTTTATTTA
TCAATTAAATTAAGATTAATTATCAAGTGCCCCTCTCCAAATATTCTTCTAAGATCTACTCGGTT
AAAGATTTATTTCTCTTTCCATCTCTTTTTCACGTTTTCTTCTCTCTTTTTTTTCTTAA
Found at i:43018 original size:58 final size:58
Alignment explanation
Indices: 42928--43038 Score: 195
Period size: 58 Copynumber: 1.9 Consensus size: 58
42918 TTTTTGCCAT
**
42928 AAGTTATCGGATTGATATTAATCTTTGAACGTAAAGGGCGGGGAGAAAAAAAAAGTTG
1 AAGTTATCGGATTGATATTAATCTTTGAACGTAAAGGAAGGGGAGAAAAAAAAAGTTG
*
42986 AAGTTATTGGATTGATATTAATCTTTGAACGTAAAGGAAGGGGAGAAAAAAAA
1 AAGTTATCGGATTGATATTAATCTTTGAACGTAAAGGAAGGGGAGAAAAAAAA
43039 GTTTGACCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.42, C:0.05, G:0.26, T:0.26
Consensus pattern (58 bp):
AAGTTATCGGATTGATATTAATCTTTGAACGTAAAGGAAGGGGAGAAAAAAAAAGTTG
Found at i:43734 original size:30 final size:29
Alignment explanation
Indices: 43647--43740 Score: 95
Period size: 29 Copynumber: 3.1 Consensus size: 29
43637 GCTCAAAAAG
43647 GCCCCTGAACT-TATACAAAACGGCCAAATAA
1 GCCCCTGAACTCT-TA-AAAA-GGCCAAATAA
**
43678 GCCCCTGAACTC-T-AATTGCAGCCAAATAA
1 GCCCCTGAACTCTTAAAAAG--GCCAAATAA
43707 GCCCCTGAACTCTTTAAAAAGGCCAAATAA
1 GCCCCTGAACTC-TTAAAAAGGCCAAATAA
43737 GCCC
1 GCCC
43741 TTTTCTGATG
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
27 1 0.02
28 2 0.04
29 21 0.40
30 14 0.26
31 12 0.23
32 3 0.06
ACGTcount: A:0.37, C:0.31, G:0.14, T:0.18
Consensus pattern (29 bp):
GCCCCTGAACTCTTAAAAAGGCCAAATAA
Done.