Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009265.1 Corchorus capsularis cultivar CVL-1 contig09286, 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: 68088
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3317 original size:25 final size:25
Alignment explanation
Indices: 3289--3336 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
3279 TGGACTTGCA
3289 TTTGAGCATATGTGTGGTTTGAAAG
1 TTTGAGCATATGTGTGGTTTGAAAG
*
3314 TTTGAGTATATGTGTGGTTTGAA
1 TTTGAGCATATGTGTGGTTTGAA
3337 TTTACTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.23, C:0.02, G:0.31, T:0.44
Consensus pattern (25 bp):
TTTGAGCATATGTGTGGTTTGAAAG
Found at i:7577 original size:3 final size:3
Alignment explanation
Indices: 7569--7608 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
7559 GTGAGGTTAA
7569 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
7609 GTGATACAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11938 original size:2 final size:2
Alignment explanation
Indices: 11927--11956 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
11917 TATGATAATT
11927 TA TA -A 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 TA TA T
11957 TCATGTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12895 original size:3 final size:3
Alignment explanation
Indices: 12887--12913 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12877 GAAGCAGCGG
12887 CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA
12914 GCACACAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:17266 original size:44 final size:44
Alignment explanation
Indices: 17168--17252 Score: 161
Period size: 44 Copynumber: 1.9 Consensus size: 44
17158 TAAATTCTTT
*
17168 TGTTTACATTATATATTAGTATATATTCTCATATACTATTTATA
1 TGTTTACATTACATATTAGTATATATTCTCATATACTATTTATA
17212 TGTTTACATTACATATTAGTATATATTCTCATATACTATTT
1 TGTTTACATTACATATTAGTATATATTCTCATATACTATTT
17253 GTGTTTTAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.33, C:0.11, G:0.05, T:0.52
Consensus pattern (44 bp):
TGTTTACATTACATATTAGTATATATTCTCATATACTATTTATA
Found at i:22200 original size:14 final size:14
Alignment explanation
Indices: 22181--22207 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22171 TTTGGGCTCG
22181 GGTTATCGGGTTCA
1 GGTTATCGGGTTCA
22195 GGTTATCGGGTTC
1 GGTTATCGGGTTC
22208 GGGTCATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.11, C:0.15, G:0.37, T:0.37
Consensus pattern (14 bp):
GGTTATCGGGTTCA
Found at i:22533 original size:32 final size:32
Alignment explanation
Indices: 22438--22604 Score: 210
Period size: 32 Copynumber: 5.2 Consensus size: 32
22428 TTTTTCACTT
* *
22438 GCGGCTCTGCCACGGCGGAGCCTCCCCACTAGG
1 GCGGCTCTGCCACGGC-TAGCCGCCCCACTAGG
*
22471 GCGGCTCTGCCACGG-TGGAGTCGCCCCACTAGG
1 GCGGCTCTGCCACGGCT--AGCCGCCCCACTAGG
* *
22504 ACGGCTCTGCCATGGCTAGCCGCCCCACTAGG
1 GCGGCTCTGCCACGGCTAGCCGCCCCACTAGG
* *
22536 ACGGCTCTGCCACGGCTAGCCGCCCCACTGGG
1 GCGGCTCTGCCACGGCTAGCCGCCCCACTAGG
** *
22568 GCGGCTCTTACACAGCTAGCCGCCCCACTAGG
1 GCGGCTCTGCCACGGCTAGCCGCCCCACTAGG
22600 GCGGC
1 GCGGC
22605 AAGGCTTTTT
Statistics
Matches: 118, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
32 76 0.64
33 41 0.35
34 1 0.01
ACGTcount: A:0.14, C:0.41, G:0.32, T:0.14
Consensus pattern (32 bp):
GCGGCTCTGCCACGGCTAGCCGCCCCACTAGG
Found at i:23080 original size:16 final size:16
Alignment explanation
Indices: 23059--23154 Score: 95
Period size: 16 Copynumber: 6.0 Consensus size: 16
23049 TTTTCATAAA
*
23059 TTTTCGGATTCGGGTT
1 TTTTCGGGTTCGGGTT
* *
23075 TTTTCGGGTTTGTGCTT
1 TTTTCGGGTTCG-GGTT
*
23092 TTTT-GGGTTCGTGTT
1 TTTTCGGGTTCGGGTT
* * *
23107 TTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTT
*
23123 TTTTCGGGTTCAGGTT
1 TTTTCGGGTTCGGGTT
*
23139 TTTTCGGGTTCAGGTT
1 TTTTCGGGTTCGGGTT
23155 CAGGCGGGTT
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
15 6 0.09
16 52 0.80
17 7 0.11
ACGTcount: A:0.04, C:0.11, G:0.31, T:0.53
Consensus pattern (16 bp):
TTTTCGGGTTCGGGTT
Found at i:23113 original size:32 final size:31
Alignment explanation
Indices: 23059--23148 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 31
23049 TTTTCATAAA
* *
23059 TTTTCGGATTCGGGTTTTTTCGGGTTTGTGCT
1 TTTTCGGGTTC-GGTTTTTTCGGGTTTGAGCT
*
23091 TTTTTGGGTTCGTGTTTTTTCGGGTTTGAGCT
1 TTTTCGGGTTCG-GTTTTTTCGGGTTTGAGCT
23123 TTTTCGGGTTCAGGTTTTTTCGGGTT
1 TTTTCGGGTTC-GGTTTTTTCGGGTT
23149 CAGGTTCAGG
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
31 1 0.02
32 50 0.96
33 1 0.02
ACGTcount: A:0.03, C:0.11, G:0.31, T:0.54
Consensus pattern (31 bp):
TTTTCGGGTTCGGTTTTTTCGGGTTTGAGCT
Found at i:23227 original size:15 final size:16
Alignment explanation
Indices: 23207--23236 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
23197 CAGGATCGGG
23207 TTTTCGGG-CGGGTTT
1 TTTTCGGGTCGGGTTT
23222 TTTTCGGGTCGGGTT
1 TTTTCGGGTCGGGTT
23237 CAGTTTGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.13, G:0.40, T:0.47
Consensus pattern (16 bp):
TTTTCGGGTCGGGTTT
Found at i:27539 original size:166 final size:163
Alignment explanation
Indices: 27234--27675 Score: 557
Period size: 166 Copynumber: 2.7 Consensus size: 163
27224 TGAGTCATTT
* *
27234 GTCAATTGAGAAATGACCAAAAAGTTTAGTTTTTTAATCCCCTCAAGAATCAAAAGTTAGAACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTACTTATTTAATCCCCTCAAGAATCAAAAGTTAG-ACAT
* * ** *
27299 TTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAGCTCATCGTCAATCCTTG
64 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAA-ATTAGTTCTCTAACTCAAAGTCAAGCCTTG
* * *
27364 ATGGGGATCTTTTATTAATTCCACTACTCTATTCAA
128 ATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* *
27400 GTCCATTGAAAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATCAAAAGTTATGACA-
1 GTCAATTGAGAAATGACCAAAAAG-TTACTTATTTAATCCCCTCAAGAATCAAAAGTTA-GACAT
* * * *
27464 TTAAGTAATCTGCCAAATAAGAAAATACGTAAAAAATAAGTTCTCTAACTCCAAAAG-CAAGCCT
64 TTAAGTAATCTGCCAAGTAGGAAAAGACG-AAAAAATTAGTTCTCTAACT-C-AAAGTCAAGCCT
*
27528 TGGTAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
126 TGATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * *
27566 GTCAATTGAGAATTGACTAAGAAGTCTAGC-TATTTAATCCCTTCAAGAATCAAAAGTTAGGACA
1 GTCAATTGAGAAATGACCAAAAAGT-TA-CTTATTTAATCCCCTCAAGAATCAAAAGTTA-GACA
* *
27630 TTTAAGTAATCTGTCAAGTGGGAAAAGACGAAAAAATTAGTTCTCT
63 TTTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAATTAGTTCTCT
27676 CGCTTCTCAT
Statistics
Matches: 238, Mismatches: 31, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
165 39 0.16
166 171 0.72
167 28 0.12
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (163 bp):
GTCAATTGAGAAATGACCAAAAAGTTACTTATTTAATCCCCTCAAGAATCAAAAGTTAGACATTT
AAGTAATCTGCCAAGTAGGAAAAGACGAAAAAATTAGTTCTCTAACTCAAAGTCAAGCCTTGATA
GGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:27749 original size:2 final size:2
Alignment explanation
Indices: 27742--27768 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27732 TAATATGTAG
27742 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
27769 TAATTAAGGA
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:38366 original size:26 final size:26
Alignment explanation
Indices: 38337--38386 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
38327 CTTCCACTTC
* * *
38337 ATTTCTGATTAATCATCTTTTGATTA
1 ATTTCTGATGAACCATCTTCTGATTA
38363 ATTTCTGATGAACCATCTTCTGAT
1 ATTTCTGATGAACCATCTTCTGAT
38387 CAAATTACTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (26 bp):
ATTTCTGATGAACCATCTTCTGATTA
Found at i:41017 original size:13 final size:13
Alignment explanation
Indices: 40999--41025 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40989 TTTTGTTTGA
40999 TTATCTGCTTTCT
1 TTATCTGCTTTCT
41012 TTATCTGCTTTCT
1 TTATCTGCTTTCT
41025 T
1 T
41026 ATAAGTTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.22, G:0.07, T:0.63
Consensus pattern (13 bp):
TTATCTGCTTTCT
Found at i:45498 original size:21 final size:21
Alignment explanation
Indices: 45474--45524 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
45464 TCTTGTCTTT
*
45474 CTTGTTCATTTCTC-AATAGTA
1 CTTGTTCAATTCTCAAAT-GTA
*
45495 CTTGTTCAATTCTCAAATGTC
1 CTTGTTCAATTCTCAAATGTA
45516 CTTGTTCAA
1 CTTGTTCAA
45525 GTAACAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.45
Consensus pattern (21 bp):
CTTGTTCAATTCTCAAATGTA
Found at i:45943 original size:18 final size:18
Alignment explanation
Indices: 45909--45951 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
45899 CAAAGTTAAG
45909 AAAAAACATAAAAACAAA
1 AAAAAACATAAAAACAAA
*
45927 AAAAATACA-AAATACAAA
1 AAAAA-ACATAAAAACAAA
45945 ACAAAAA
1 A-AAAAA
45952 AAATGAGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.81, C:0.12, G:0.00, T:0.07
Consensus pattern (18 bp):
AAAAAACATAAAAACAAA
Found at i:50065 original size:2 final size:2
Alignment explanation
Indices: 50010--50045 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
50000 GTATTTACAC
50010 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
50046 GCTCTAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53725 original size:10 final size:10
Alignment explanation
Indices: 53697--53726 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
53687 CCAAATTTCT
53697 TTAAGTGTTC
1 TTAAGTGTTC
53707 TTAAGGTGTTC
1 TTAA-GTGTTC
53718 TTAAGTGTT
1 TTAAGTGTT
53727 TTGTCTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.20, C:0.07, G:0.23, T:0.50
Consensus pattern (10 bp):
TTAAGTGTTC
Found at i:55451 original size:18 final size:19
Alignment explanation
Indices: 55424--55459 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
55414 ATTTACTAAC
55424 ACTTTAATTTTT-TTTTTT
1 ACTTTAATTTTTCTTTTTT
*
55442 ACTTTCATTTTTCTTTTT
1 ACTTTAATTTTTCTTTTT
55460 CATTTTAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (19 bp):
ACTTTAATTTTTCTTTTTT
Found at i:64634 original size:93 final size:93
Alignment explanation
Indices: 64532--64709 Score: 313
Period size: 93 Copynumber: 1.9 Consensus size: 93
64522 AATTAAATTA
*
64532 GTAATATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAAT-AAAATTAGAGTTTT
1 GTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATT-GAGTTTT
64596 TAATTGAGTAAAACTATAAAAGTAAAATG
65 TAATTGAGTAAAACTATAAAAGTAAAATG
*
64625 GTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATTGAGTTTTT
1 GTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATTGAGTTTTT
*
64690 AGTTGAGTAAAACTATAAAA
66 AATTGAGTAAAACTATAAAA
64710 ATTTAAACAA
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
93 75 0.93
94 6 0.07
ACGTcount: A:0.51, C:0.01, G:0.15, T:0.34
Consensus pattern (93 bp):
GTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATTGAGTTTTT
AATTGAGTAAAACTATAAAAGTAAAATG
Found at i:66501 original size:22 final size:22
Alignment explanation
Indices: 66476--66520 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
66466 AAAAATTCCC
*
66476 AATTCTCTTGAGAACTAAATCA
1 AATTCTATTGAGAACTAAATCA
*
66498 AATTCTATTGATAACTAAATCA
1 AATTCTATTGAGAACTAAATCA
66520 A
1 A
66521 GAATTCCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (22 bp):
AATTCTATTGAGAACTAAATCA
Found at i:67236 original size:23 final size:23
Alignment explanation
Indices: 67185--67229 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
67175 GTATCAAGAG
67185 AGAAAGAAGGAAGAAGAAAGGAA
1 AGAAAGAAGGAAGAAGAAAGGAA
*
67208 AGAAAGAA-GAAG-AGACAGGAA
1 AGAAAGAAGGAAGAAGAAAGGAA
67229 A
1 A
67230 TGGAAAGGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 4 0.19
23 8 0.38
ACGTcount: A:0.64, C:0.02, G:0.33, T:0.00
Consensus pattern (23 bp):
AGAAAGAAGGAAGAAGAAAGGAA
Found at i:67703 original size:13 final size:13
Alignment explanation
Indices: 67685--67711 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
67675 CTTTATAACC
67685 TCATAAATCATAT
1 TCATAAATCATAT
67698 TCATAAATCATAT
1 TCATAAATCATAT
67711 T
1 T
67712 TATTATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TCATAAATCATAT
Done.