Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010358.1 Corchorus capsularis cultivar CVL-1 contig10379, 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: 76020
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:1567 original size:2 final size:2
Alignment explanation
Indices: 1555--1585 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
1545 TACAACATCG
1555 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
1586 TTAAAACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3004 original size:34 final size:35
Alignment explanation
Indices: 2960--3045 Score: 120
Period size: 36 Copynumber: 2.5 Consensus size: 35
2950 GCATTGATTT
* *
2960 TCTCTTAAATGATAATTC-TTTTTTTTTGGTGGTA
1 TCTCTCAAATGATAATTCTTTTTTTTTTGGCGGTA
* *
2994 TCTCTCAAATGATATTTCTTTTTTTTTTTTGCGGTA
1 TCTCTCAAATGATAATTC-TTTTTTTTTTGGCGGTA
3030 TCTCTCAAATGATAAT
1 TCTCTCAAATGATAAT
3046 CCATACTTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
34 16 0.36
36 29 0.64
ACGTcount: A:0.22, C:0.13, G:0.12, T:0.53
Consensus pattern (35 bp):
TCTCTCAAATGATAATTCTTTTTTTTTTGGCGGTA
Found at i:3682 original size:11 final size:11
Alignment explanation
Indices: 3662--3705 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
3652 ATGTATATTC
*
3662 ATAATAAATTT
1 ATAATTAATTT
3673 ATAATTAATTT
1 ATAATTAATTT
3684 ATAATT-ATTT
1 ATAATTAATTT
*
3694 GATAATTTATTT
1 -ATAATTAATTT
3706 TACATAGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 4 0.13
11 22 0.73
12 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
ATAATTAATTT
Found at i:5507 original size:14 final size:13
Alignment explanation
Indices: 5479--5504 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5469 CTAAAAAAGC
5479 AATTTAATGTTTT
1 AATTTAATGTTTT
5492 AATTTAATGTTTT
1 AATTTAATGTTTT
5505 TAAAGATGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
AATTTAATGTTTT
Found at i:6649 original size:22 final size:22
Alignment explanation
Indices: 6613--6663 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
6603 CTTACAACAT
*
6613 TACT-AAAATTTTAATAAAGGC
1 TACTAAAAATTGTAATAAAGGC
* *
6634 TACTAAAAATTGTAATAAGGGT
1 TACTAAAAATTGTAATAAAGGC
6656 TACTAAAA
1 TACTAAAA
6664 TGTTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (22 bp):
TACTAAAAATTGTAATAAAGGC
Found at i:6719 original size:21 final size:21
Alignment explanation
Indices: 6693--6751 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
6683 AAGAAAGCAG
6693 GGTTACTAAAATGTTTAGTAA
1 GGTTACTAAAATGTTTAGTAA
* *
6714 GGTTACTTAAAA-GCTTATTAA
1 GGTTAC-TAAAATGTTTAGTAA
*
6735 -CTTACTAATAATGTTTA
1 GGTTACTAA-AATGTTTA
6752 TATGATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 3 0.10
20 6 0.19
21 17 0.55
22 5 0.16
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (21 bp):
GGTTACTAAAATGTTTAGTAA
Found at i:7029 original size:23 final size:23
Alignment explanation
Indices: 6979--7048 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
6969 ATAAGATTTC
* * *
6979 TAAAACACTTAATAAGGTTATTA
1 TAAAAAACTTCATAAGGTTACTA
*
7002 AAAAAAACTTCATAAGGTTACTA
1 TAAAAAACTTCATAAGGTTACTA
7025 T--AAAA-TTCATAA-GTTAACTA
1 TAAAAAACTTCATAAGGTT-ACTA
7045 TAAA
1 TAAA
7049 TCTTACAAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 3 0.08
20 12 0.31
21 4 0.10
22 1 0.03
23 19 0.49
ACGTcount: A:0.51, C:0.10, G:0.07, T:0.31
Consensus pattern (23 bp):
TAAAAAACTTCATAAGGTTACTA
Found at i:7035 original size:20 final size:21
Alignment explanation
Indices: 7005--7048 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
6995 GTTATTAAAA
7005 AAAACTTCATAAGGTT-ACTAT
1 AAAACTTCATAA-GTTAACTAT
7026 AAAA-TTCATAAGTTAACTAT
1 AAAACTTCATAAGTTAACTAT
7046 AAA
1 AAA
7049 TCTTACAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 15 0.68
21 4 0.18
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (21 bp):
AAAACTTCATAAGTTAACTAT
Found at i:7758 original size:24 final size:25
Alignment explanation
Indices: 7717--7766 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
7707 ACTATAAAAC
*
7717 TTGCTTACTAAAAAGGTTTTAAGGT
1 TTGCTTACAAAAAAGGTTTTAAGGT
7742 TTGCTTA-AAAAAAGGTTTTAAGGT
1 TTGCTTACAAAAAAGGTTTTAAGGT
7766 T
1 T
7767 ATTAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (25 bp):
TTGCTTACAAAAAAGGTTTTAAGGT
Found at i:7771 original size:22 final size:24
Alignment explanation
Indices: 7726--7775 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
7716 CTTGCTTACT
*
7726 AAAAAGGTTTTAAGGTTTGCTTAA
1 AAAAAGGTTTTAAGGTTTGATTAA
7750 AAAAAGGTTTTAAGG-TT-ATTAA
1 AAAAAGGTTTTAAGGTTTGATTAA
7772 AAAA
1 AAAA
7776 TTTATTAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 8 0.32
23 2 0.08
24 15 0.60
ACGTcount: A:0.46, C:0.02, G:0.18, T:0.34
Consensus pattern (24 bp):
AAAAAGGTTTTAAGGTTTGATTAA
Found at i:8168 original size:16 final size:15
Alignment explanation
Indices: 8147--8176 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
8137 CTACAAATTT
8147 ATAAAGATTTAGTAAA
1 ATAAAGATTT-GTAAA
8163 ATAAAGATTTGTAA
1 ATAAAGATTTGTAA
8177 TATTTTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (15 bp):
ATAAAGATTTGTAAA
Found at i:9137 original size:3 final size:3
Alignment explanation
Indices: 9129--9167 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
9119 CTTGCTGGTC
* * *
9129 CTG CTG CTG CTG CTG CTG CTG TTG CTG TTG CTG CCG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
9168 AGGCTGAGGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.31, G:0.33, T:0.36
Consensus pattern (3 bp):
CTG
Found at i:17954 original size:1 final size:1
Alignment explanation
Indices: 17948--17972 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
17938 TCTTATGTAC
17948 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
17973 CTTTAATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21324 original size:74 final size:74
Alignment explanation
Indices: 21236--21384 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
21226 GCTTACTCAC
21236 CGGCTTTACAAGTCAGAACAAATATTACAGGAGAACCCTGTATGTCAAAACTTAAACCTCTAAAT
1 CGGCTTTACAAGTCAGAACAAATATTACAGGAGAACCCTGTATGTCAAAACTTAAACCTCTAAAT
21301 ACAGCAATT
66 ACAGCAATT
21310 CGGCTTTACAAGTCAGAACAAATATTACAGGAGAACCCTGTATGTCAAAACTTAAACCTCTAAAT
1 CGGCTTTACAAGTCAGAACAAATATTACAGGAGAACCCTGTATGTCAAAACTTAAACCTCTAAAT
21375 ACAGCAATT
66 ACAGCAATT
21384 C
1 C
21385 TATGACTTTG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.24
Consensus pattern (74 bp):
CGGCTTTACAAGTCAGAACAAATATTACAGGAGAACCCTGTATGTCAAAACTTAAACCTCTAAAT
ACAGCAATT
Found at i:27505 original size:37 final size:37
Alignment explanation
Indices: 27450--27528 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
27440 GCCCTGTACT
* *
27450 TTGTAAATTTAGGATAAATTGCCCACTTAATCTTAAA
1 TTGTGAATTTAGGATAAATTGCCCACTTAACCTTAAA
*
27487 TTGTGAATTTAGGATAAATTGCTCACTTAACCTTAAA
1 TTGTGAATTTAGGATAAATTGCCCACTTAACCTTAAA
27524 TTGTG
1 TTGTG
27529 CGGCTTTATC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (37 bp):
TTGTGAATTTAGGATAAATTGCCCACTTAACCTTAAA
Found at i:29062 original size:40 final size:40
Alignment explanation
Indices: 29000--29080 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
28990 ACTTGACCCT
*
29000 CCTAATAATTAAGAAAATAAATTAAA-TCTAGATTTAGCCC
1 CCTAATAATTAAGAAAAGAAATTAAATTC-AGATTTAGCCC
*
29040 CCTAATAATTAA-ATTAAGAAATTAAATTCAGATTTAGCCC
1 CCTAATAATTAAGA-AAAGAAATTAAATTCAGATTTAGCCC
29080 C
1 C
29081 TAGTTATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
39 1 0.03
40 34 0.92
41 2 0.05
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (40 bp):
CCTAATAATTAAGAAAAGAAATTAAATTCAGATTTAGCCC
Found at i:31583 original size:1 final size:1
Alignment explanation
Indices: 31577--31608 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
31567 GGTTTCAACG
*
31577 AAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31609 CTAGAACTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:32371 original size:14 final size:14
Alignment explanation
Indices: 32348--32391 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
32338 ACCTAACTTC
32348 AAATTCCCAAAAGA
1 AAATTCCCAAAAGA
*
32362 AAA-TCACCAAAAAA
1 AAATTC-CCAAAAGA
32376 AAATTCCCAAAAGA
1 AAATTCCCAAAAGA
32390 AA
1 AA
32392 TACTTGGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.64, C:0.20, G:0.05, T:0.11
Consensus pattern (14 bp):
AAATTCCCAAAAGA
Found at i:59462 original size:19 final size:18
Alignment explanation
Indices: 59438--59478 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
59428 CGCAATCTCT
59438 AAAAAAAGAAAAACAAAAG
1 AAAAAAAG-AAAACAAAAG
*
59457 AAAAAAAGAAAAGAAAAG
1 AAAAAAAGAAAACAAAAG
59475 AAAA
1 AAAA
59479 GAAAAGGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAACAAAAG
Found at i:59468 original size:5 final size:5
Alignment explanation
Indices: 59441--59484 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
59431 AATCTCTAAA
*
59441 AAAAG AAAAAC AAAAG -AAA- AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
59485 GAAGCTAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
4 6 0.18
5 24 0.71
6 4 0.12
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:75991 original size:2 final size:2
Alignment explanation
Indices: 75984--76019 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
75974 ATGACGGTGA
75984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A
76020 C
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.