Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007100.1 Corchorus capsularis cultivar CVL-1 contig07121, 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: 41081
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Found at i:1425 original size:13 final size:13
Alignment explanation
Indices: 1407--1436 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1397 GCAAGCCAAG
1407 ATGAACCAAAAAC
1 ATGAACCAAAAAC
1420 ATGAACCAAAAAC
1 ATGAACCAAAAAC
1433 ATGA
1 ATGA
1437 GAGTGTGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.20, G:0.10, T:0.10
Consensus pattern (13 bp):
ATGAACCAAAAAC
Found at i:1571 original size:17 final size:17
Alignment explanation
Indices: 1549--1583 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1539 AGAGTTTTGT
1549 AAATTGACATGCTAAGC
1 AAATTGACATGCTAAGC
1566 AAATTGACATGCTAAGC
1 AAATTGACATGCTAAGC
1583 A
1 A
1584 GTTATACGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (17 bp):
AAATTGACATGCTAAGC
Found at i:2013 original size:25 final size:25
Alignment explanation
Indices: 1984--2033 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1974 AAGTGAAGCC
1984 CAGATCATGCACAAAACCCAGATCA
1 CAGATCATGCACAAAACCCAGATCA
2009 CAGATCATGCACAAAACCCAGATCA
1 CAGATCATGCACAAAACCCAGATCA
2034 TGTTGCAGCA
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:0.44, C:0.32, G:0.12, T:0.12
Consensus pattern (25 bp):
CAGATCATGCACAAAACCCAGATCA
Found at i:7628 original size:11 final size:11
Alignment explanation
Indices: 7612--7643 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
7602 TCGAAGTTCG
7612 TATTTGAAGAT
1 TATTTGAAGAT
7623 TATTTGAAGAT
1 TATTTGAAGAT
*
7634 AATTTGAAGA
1 TATTTGAAGA
7644 ATTGAAGACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (11 bp):
TATTTGAAGAT
Found at i:7650 original size:19 final size:18
Alignment explanation
Indices: 7626--7664 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
7616 TGAAGATTAT
*
7626 TTGAAGATAATTTGAAGAA
1 TTGAAGACAA-TTGAAGAA
*
7645 TTGAAGACCATTGAAGAA
1 TTGAAGACAATTGAAGAA
7663 TT
1 TT
7665 ATTTCAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAA
Found at i:9032 original size:21 final size:20
Alignment explanation
Indices: 9008--9051 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
8998 TTGCCATAGA
*
9008 TTTAGATTTAATTTACTTTGC
1 TTTAGATTTAATTTA-ATTGC
**
9029 TTTATTTTTAATTTAATTGC
1 TTTAGATTTAATTTAATTGC
9049 TTT
1 TTT
9052 CTTTTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.64
Consensus pattern (20 bp):
TTTAGATTTAATTTAATTGC
Found at i:9050 original size:20 final size:21
Alignment explanation
Indices: 9014--9061 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
9004 TAGATTTAGA
*
9014 TTTAATTTACTTTGCTTTATT
1 TTTAATTTACATTGCTTTATT
*
9035 TTTAATTTA-ATTGCTTTCTT
1 TTTAATTTACATTGCTTTATT
9055 TTTAATT
1 TTTAATT
9062 GATAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.21, C:0.08, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTAATTTACATTGCTTTATT
Found at i:9573 original size:166 final size:165
Alignment explanation
Indices: 9253--9655 Score: 558
Period size: 166 Copynumber: 2.4 Consensus size: 165
9243 TGAGTCATTT
*
9253 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCACTCAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* ** * ** * *
9318 TTAAGTAATCTGCCAAGTAGGTAAAGACGAAAAAGATTAGTTCTCTAGCTCATCATCAATCCTTG
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAGAAAAGTTCTCTAACTCAAAAGCAAGCCTTG
* * * *
9383 ATGGGGATCTTGTATTAGTTCCACTACCCTATTCAA
130 ATAGGGACCTTGTATGAGTTCCACTACCCTATTAAA
* * *
9419 GTCCATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAAGAATCAAAAGTTTGGACAT
1 GTCAATTGAGAAATGACCAAAAAG-TTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
*
9484 TTAAGTAATCTGCCAAGTAGGAAAAGATGAAAAA-AAAAGTTCTCTAACTCCAAAAGCAAGCCTT
65 TTAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAGAAAAGTTCTCTAACT-CAAAAGCAAGCCTT
* * *
9548 GGTAGGGACCTTTTAGTGA-TTCCACTACTCTATTAAA
129 GATAGGGACCTTGTA-TGAGTTCCACTACCCTATTAAA
*
9585 GTCAATTGAGAAATGACCAAAAAGTCTAGTTATTTAATCCCCTTAAGAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGT-TAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
9650 TTAAGT
65 TTAAGT
9656 TTAAACTTTA
Statistics
Matches: 209, Mismatches: 25, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
165 13 0.06
166 194 0.93
167 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (165 bp):
GTCAATTGAGAAATGACCAAAAAGTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACATT
TAAGTAATCTGCCAAGTAGGAAAAGACGAAAAAGAAAAGTTCTCTAACTCAAAAGCAAGCCTTGA
TAGGGACCTTGTATGAGTTCCACTACCCTATTAAA
Found at i:10023 original size:45 final size:45
Alignment explanation
Indices: 9968--10053 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
9958 ACTTCTCCAG
*
9968 CTCATCATTAATCCGGGGTAGGGATCTTTTAGTAATTCCACCCAA
1 CTCATCATTAATCCGAGGTAGGGATCTTTTAGTAATTCCACCCAA
* *
10013 CTCATTATTAATTCGAGGTAGGGATCTTTTAGTAATTCCAC
1 CTCATCATTAATCCGAGGTAGGGATCTTTTAGTAATTCCAC
10054 TACTCTATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (45 bp):
CTCATCATTAATCCGAGGTAGGGATCTTTTAGTAATTCCACCCAA
Found at i:19690 original size:14 final size:15
Alignment explanation
Indices: 19667--19700 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
19657 AATTTAAAAA
*
19667 TATATTTATCTAT-C
1 TATATCTATCTATAC
19681 TATATCTATCTATAC
1 TATATCTATCTATAC
19696 TATAT
1 TATAT
19701 ATAAAAGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATCTATCTATAC
Found at i:24148 original size:19 final size:18
Alignment explanation
Indices: 24115--24151 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
24105 TTGAAATAAT
24115 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
24133 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
24152 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:25392 original size:12 final size:12
Alignment explanation
Indices: 25375--25404 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
25365 GGAATAAAAG
25375 ATCAATCCATCA
1 ATCAATCCATCA
25387 ATCAATCCATCA
1 ATCAATCCATCA
25399 A-CAATC
1 ATCAATC
25405 AAATTGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.23
Consensus pattern (12 bp):
ATCAATCCATCA
Found at i:34734 original size:30 final size:30
Alignment explanation
Indices: 34672--34841 Score: 295
Period size: 30 Copynumber: 5.6 Consensus size: 30
34662 CATGGTGTAT
*
34672 ATGACAACTTCTGGTGTCAATTGAATAAATC
1 ATGACAACTTCTGGTGTCAATTGCA-AAATC
34703 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
34733 ATGACAACTTCAGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* *
34763 ATGAGAACTTCTAGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
34793 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
34823 ATGACAACTTCTGGTGTCA
1 ATGACAACTTCTGGTGTCA
34842 TTATGGGACT
Statistics
Matches: 132, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 108 0.82
31 24 0.18
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGCAAAATC
Found at i:35760 original size:38 final size:38
Alignment explanation
Indices: 35709--35785 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
35699 GATCCCCTTT
*
35709 ACATTTAATGCTAATTTACTTTACTTGCAAGCAAAGTA
1 ACATTTAATGCTAATCTACTTTACTTGCAAGCAAAGTA
*
35747 ACATTTAATGCTAATCTGCTTTACTTGCAAGCAAAGTA
1 ACATTTAATGCTAATCTACTTTACTTGCAAGCAAAGTA
35785 A
1 A
35786 AATCTAACGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (38 bp):
ACATTTAATGCTAATCTACTTTACTTGCAAGCAAAGTA
Found at i:36867 original size:2 final size:2
Alignment explanation
Indices: 36860--36888 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36850 AACTAGTATG
36860 TA 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 TA T
36889 TGTGGTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37662 original size:23 final size:23
Alignment explanation
Indices: 37632--37677 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
37622 TGGTTTAATT
37632 TTTAAATT-TTATTTTTATTTAAA
1 TTTAAATTATTA-TTTTATTTAAA
37655 TTTAAATTATTATTTTATTTAAA
1 TTTAAATTATTATTTTATTTAAA
37678 AAAATTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTAAATTATTATTTTATTTAAA
Done.