Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006443.1 Corchorus capsularis cultivar CVL-1 contig06464, 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: 26324
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:1676 original size:20 final size:21
Alignment explanation
Indices: 1643--1681 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1633 TGCAAAATAG
*
1643 GGTAAAAACATATATAAAAGT
1 GGTAAAAACATATAGAAAAGT
*
1664 GGTAAAAA-GTATAGAAAA
1 GGTAAAAACATATAGAAAA
1682 TAGCTATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.59, C:0.03, G:0.18, T:0.21
Consensus pattern (21 bp):
GGTAAAAACATATAGAAAAGT
Found at i:4657 original size:21 final size:21
Alignment explanation
Indices: 4613--4658 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
4603 TGAGAACGAG
* **
4613 GAAGAAGAAACAGCTGATTCA
1 GAAGAAGAAAAAGCTGATGAA
*
4634 GAAGAAGAAAAATCTGATGAA
1 GAAGAAGAAAAAGCTGATGAA
4655 GAAG
1 GAAG
4659 TTGATGAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.09, G:0.26, T:0.13
Consensus pattern (21 bp):
GAAGAAGAAAAAGCTGATGAA
Found at i:6729 original size:76 final size:76
Alignment explanation
Indices: 6601--6751 Score: 216
Period size: 76 Copynumber: 2.0 Consensus size: 76
6591 TTTCAACGTC
* *
6601 ATAAATTGACAGATTTGAAAGACTTGCGATTAATGAGGAATATGATCGTTGGAAGCAGATCTAAG
1 ATAAATTGACAGATTTGAAAGACTTGCGATTAATGAGGAATATGACCATTGGAAGCAGATCTAAG
6666 TATTTAAGGAA
66 TATTTAAGGAA
* * * *
6677 ATAAATTGACAGATTTGAAAGATTTGC-ATTTAATGTGGAGA-ATGACCATTGGAGGCAGATCTG
1 ATAAATTGACAGATTTGAAAGACTTGCGA-TTAATGAGGA-ATATGACCATTGGAAGCAGATCTA
6740 AGTATTTAAGGA
64 AGTATTTAAGGA
6752 CCAAAAAGAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
75 1 0.01
76 65 0.97
77 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.30
Consensus pattern (76 bp):
ATAAATTGACAGATTTGAAAGACTTGCGATTAATGAGGAATATGACCATTGGAAGCAGATCTAAG
TATTTAAGGAA
Found at i:20393 original size:27 final size:26
Alignment explanation
Indices: 20323--20394 Score: 92
Period size: 26 Copynumber: 2.7 Consensus size: 26
20313 GATCACCTCG
20323 GGGGCATTTTGGTCATCTTTACACTAA
1 GGGGCATTTTGGTCAT-TTTACACTAA
* *
20350 -GGGCATTTAGGTCATTTTCACATTAA
1 GGGGCATTTTGGTCATTTT-ACACTAA
*
20376 GGGGCATTTTGGTAATTTT
1 GGGGCATTTTGGTCATTTT
20395 GAGTTCGCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 3 0.08
26 20 0.51
27 16 0.41
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (26 bp):
GGGGCATTTTGGTCATTTTACACTAA
Found at i:20825 original size:20 final size:18
Alignment explanation
Indices: 20790--20832 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
20780 CAAAATACAA
* *
20790 AAAAATTATTAGAAAATG
1 AAAAATTATTAAAAAAAG
20808 AAAAATTATAATAAAAAAAG
1 AAAAATTAT--TAAAAAAAG
20828 AAAAA
1 AAAAA
20833 AAAGAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
20 12 0.57
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAAAATTATTAAAAAAAG
Found at i:20834 original size:9 final size:9
Alignment explanation
Indices: 20820--20850 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
20810 AAATTATAAT
20820 AAAAAAAGA
1 AAAAAAAGA
20829 AAAAAAAGA
1 AAAAAAAGA
20838 AGAAAAAAGA
1 A-AAAAAAGA
20848 AAA
1 AAA
20851 GTTTCTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:22308 original size:31 final size:31
Alignment explanation
Indices: 22273--22334 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
22263 AATTATCTCG
*
22273 GCAATCGATTTC-ATAAAAATGTAAAAATGTA
1 GCAATCGATTTCTATAAAAAT-AAAAAATGTA
* *
22304 GCAATTGATTTCTATTAAAATAAAAAATGTA
1 GCAATCGATTTCTATAAAAATAAAAAATGTA
22335 ACATATTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.32
Consensus pattern (31 bp):
GCAATCGATTTCTATAAAAATAAAAAATGTA
Found at i:23426 original size:16 final size:15
Alignment explanation
Indices: 23405--23434 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
23395 CATTTAGCCG
23405 AAAGAAACAGAAAAGA
1 AAAGAAACA-AAAAGA
23421 AAAGAAACAAAAAG
1 AAAGAAACAAAAAG
23435 GGGAAGAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.77, C:0.07, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAGAAACAAAAAGA
Found at i:24847 original size:13 final size:14
Alignment explanation
Indices: 24829--24857 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
24819 ATAATCAGAC
24829 TTTGCATTCAT-CA
1 TTTGCATTCATGCA
24842 TTTGCATTCATGCA
1 TTTGCATTCATGCA
24856 TT
1 TT
24858 GAATAGAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTGCATTCATGCA
Done.