Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007461.1 Corchorus capsularis cultivar CVL-1 contig07482, 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: 30101
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:18013 original size:87 final size:88
Alignment explanation
Indices: 17910--18073 Score: 260
Period size: 87 Copynumber: 1.9 Consensus size: 88
17900 GCAGGGTTTA
* * *
17910 AAAAAATGATGTTTACTCATATCATGAATTCATATGACAATTATGTACTAAGTCAAATCT-TCAA
1 AAAAAATGATGTTTACTCATATCATGAATTCATATAACAATTATGCACTAAGTCAAATCTCCCAA
17974 TCTTTAAGAAAAAGTTATTGGTT
66 TCTTTAAGAAAAAGTTATTGGTT
*
17997 AAAAAAT-ATGTCTTACTCATGTCATGAATTCATATAACAATTATGCACTAAGTCAAATCTCCCA
1 AAAAAATGATGT-TTACTCATATCATGAATTCATATAACAATTATGCACTAAGTCAAATCTCCCA
*
18061 ATTTTTAAGAAAA
65 ATCTTTAAGAAAA
18074 TCCAAGAATG
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
86 4 0.06
87 52 0.74
88 14 0.20
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (88 bp):
AAAAAATGATGTTTACTCATATCATGAATTCATATAACAATTATGCACTAAGTCAAATCTCCCAA
TCTTTAAGAAAAAGTTATTGGTT
Found at i:18146 original size:15 final size:14
Alignment explanation
Indices: 18120--18171 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
18110 TATAAATGAC
18120 TAAATATAATATTAA
1 TAAAT-TAATATTAA
*
18135 TTAAATTAATATTCA
1 -TAAATTAATATTAA
*
18150 TAAATTAATTCTTAA
1 TAAATTAA-TATTAA
18165 -AAATTAA
1 TAAATTAA
18172 AAATGAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 15 0.47
15 12 0.38
16 5 0.16
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAATTAATATTAA
Found at i:19756 original size:2 final size:2
Alignment explanation
Indices: 19738--19778 Score: 64
Period size: 2 Copynumber: 19.5 Consensus size: 2
19728 GTTAAAAATA
19738 AT AT AT AGT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A
19779 GTAATAGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 33 0.89
3 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:19756 original size:12 final size:12
Alignment explanation
Indices: 19739--19799 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
19729 TTAAAAATAA
19739 TATATAGTATAG
1 TATATAGTATAG
19751 TATATA-TATA-
1 TATATAGTATAG
*
19761 TATATA-TATATA
1 TATATAGTATA-G
19773 TATATAGTAATAG
1 TATATAGT-ATAG
19786 TA-ATAGTAATAG
1 TATATAGT-ATAG
19798 TA
1 TA
19800 AGCCGCTCCC
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 10 0.23
11 4 0.09
12 24 0.55
13 3 0.07
14 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (12 bp):
TATATAGTATAG
Found at i:19785 original size:6 final size:6
Alignment explanation
Indices: 19776--19800 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19766 ATATATATAT
19776 ATAGTA ATAGTA ATAGTA ATAGTA A
1 ATAGTA ATAGTA ATAGTA ATAGTA A
19801 GCCGCTCCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (6 bp):
ATAGTA
Found at i:24504 original size:42 final size:43
Alignment explanation
Indices: 24443--24550 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 43
24433 GATTACCATT
* **
24443 TTACTCTTTTACTAATTACT-ATTTTCTGCT-CTTTTTTACTGA
1 TTACTCTTTTACTTATTACTGATTGCCTGCTGC-TTTTTACTGA
* **
24485 TTACTCTTTTACTTTTTACTGATTGCCTTTTGCTTTTTACTGA
1 TTACTCTTTTACTTATTACTGATTGCCTGCTGCTTTTTACTGA
* *
24528 TTAC-CTTTTACTTCTTGCTGATT
1 TTACTCTTTTACTTATTACTGATT
24551 AGCTTTTTAC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
42 35 0.62
43 20 0.36
44 1 0.02
ACGTcount: A:0.16, C:0.19, G:0.07, T:0.57
Consensus pattern (43 bp):
TTACTCTTTTACTTATTACTGATTGCCTGCTGCTTTTTACTGA
Found at i:24514 original size:21 final size:21
Alignment explanation
Indices: 24475--24684 Score: 148
Period size: 21 Copynumber: 10.0 Consensus size: 21
24465 TTTCTGCTCT
24475 TTTTTACTGATTACTCTTTTAC
1 TTTTTACTGATTAC-CTTTTAC
* *
24497 TTTTTACTGATTGCCTTTTGC
1 TTTTTACTGATTACCTTTTAC
24518 TTTTTACTGATTACCTTTTAC
1 TTTTTACTGATTACCTTTTAC
* * *
24539 TTCTTGCTGATTAGCTTTTTAC
1 TTTTTACTGATTA-CCTTTTAC
* * *
24561 TCTTTACTGATCACTTTTTTAC
1 TTTTTACTGATTAC-CTTTTAC
* *
24583 -TCTTACTGATTTCCTTTTAC
1 TTTTTACTGATTACCTTTTAC
*
24603 TTATTACT-A-T---TTTTA-
1 TTTTTACTGATTACCTTTTAC
* *
24618 TTCTTACTGATTACTATTTTAC
1 TTTTTACTGATTAC-CTTTTAC
* * *
24640 CTTTTACTGATTATCATTACTT-T
1 TTTTTACTGATTA-CCTT--TTAC
*
24663 TTTTTATTGATTACCTTTTAC
1 TTTTTACTGATTACCTTTTAC
24684 T
1 T
24685 ATTTCATTCT
Statistics
Matches: 149, Mismatches: 25, Indels: 29
0.73 0.12 0.14
Matches are distributed among these distances:
15 7 0.05
16 6 0.04
17 1 0.01
19 1 0.01
20 9 0.06
21 58 0.39
22 53 0.36
23 12 0.08
24 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.58
Consensus pattern (21 bp):
TTTTTACTGATTACCTTTTAC
Found at i:24567 original size:43 final size:43
Alignment explanation
Indices: 24477--24603 Score: 159
Period size: 43 Copynumber: 3.0 Consensus size: 43
24467 TCTGCTCTTT
* * *
24477 TTTACTGATTACTCTTTTACTTTTTACTGATTGCCTTTTGCTT
1 TTTACTGATTACTCTTTTACTTCTTACTGATTGCCTTTTACTC
* *
24520 TTTACTGATTAC-CTTTTACTTCTTGCTGATTAGCTTTTTACTC
1 TTTACTGATTACTCTTTTACTTCTTACTGATT-GCCTTTTACTC
* * *
24563 TTTACTGATCACTTTTTTAC-TCTTACTGATTTCCTTTTACT
1 TTTACTGATTACTCTTTTACTTCTTACTGATTGCCTTTTACT
24604 TATTACTATT
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
42 25 0.35
43 41 0.57
44 6 0.08
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.56
Consensus pattern (43 bp):
TTTACTGATTACTCTTTTACTTCTTACTGATTGCCTTTTACTC
Found at i:24733 original size:22 final size:21
Alignment explanation
Indices: 24692--24741 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
24682 ACTATTTCAT
* *
24692 TCTTTACTGATTATCTTTTTAC
1 TCTTTACTGATTACCCTTTT-C
*
24714 TTTTTACTGATTACCCTTTTC
1 TCTTTACTGATTACCCTTTTC
24735 TCTTTAC
1 TCTTTAC
24742 CATTCTCCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.16, C:0.22, G:0.04, T:0.58
Consensus pattern (21 bp):
TCTTTACTGATTACCCTTTTC
Found at i:24817 original size:36 final size:36
Alignment explanation
Indices: 24715--24908 Score: 225
Period size: 36 Copynumber: 5.4 Consensus size: 36
24705 TCTTTTTACT
* * * *
24715 TTTTACTGATTACCCTTTTC-TCTTTACCATTCTCC
1 TTTTACTGATTACTCTTTACTTTTTTACCATTCTTC
*
24750 CTTTACTGATTACTCTTTAC-TTTTTACCATTCTTC
1 TTTTACTGATTACTCTTTACTTTTTTACCATTCTTC
* * *
24785 TTTAACTGATTACTTTTTTCTTTTTTACCATTCTTC
1 TTTTACTGATTACTCTTTACTTTTTTACCATTCTTC
24821 TTTTACTGATTACTCTTTACTTTTTTACCATTCTTC
1 TTTTACTGATTACTCTTTACTTTTTTACCATTCTTC
* * *
24857 TTTTGCTGATTACTTTTTACTTCTTTT--CATTTTTAC
1 TTTTACTGATTACTCTTTACTT-TTTTACCATTCTT-C
*
24893 TCTTTACTAATTACTC
1 T-TTTACTGATTACTC
24909 CTGATTACTG
Statistics
Matches: 137, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
35 52 0.38
36 70 0.51
37 15 0.11
ACGTcount: A:0.16, C:0.23, G:0.03, T:0.57
Consensus pattern (36 bp):
TTTTACTGATTACTCTTTACTTTTTTACCATTCTTC
Found at i:24833 original size:21 final size:21
Alignment explanation
Indices: 24773--24833 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
24763 TCTTTACTTT
*
24773 TTACCATTCTTCTTTAACTGA
1 TTACCATTCTTCTTTTACTGA
* *
24794 TTA-CTTTTTTC-TTT--T--
1 TTACCATTCTTCTTTTACTGA
24809 TTACCATTCTTCTTTTACTGA
1 TTACCATTCTTCTTTTACTGA
24830 TTAC
1 TTAC
24834 TCTTTACTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 12
0.63 0.11 0.26
Matches are distributed among these distances:
15 3 0.10
16 6 0.21
17 4 0.14
19 3 0.10
20 6 0.21
21 7 0.24
ACGTcount: A:0.18, C:0.21, G:0.03, T:0.57
Consensus pattern (21 bp):
TTACCATTCTTCTTTTACTGA
Found at i:24976 original size:55 final size:55
Alignment explanation
Indices: 24912--25204 Score: 487
Period size: 55 Copynumber: 5.3 Consensus size: 55
24902 ATTACTCCTG
* * *
24912 ATTACTGATTTACTGATTACTATTACCTTGACTATGATTAATTTGTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
* *
24967 ATTAATGATTTACTGATTACTATTACCTTGACTCTGATTAATCTGTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
* *
25022 ATTACCGATTTACTGATTACTATTACCTTGACTCTGATTAATCCCTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
25077 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
* *
25132 ATTACTGACTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
* *
25187 AATACTGACTTACTGATT
1 ATTACTGATTTACTGATT
25205 GCATCTTTCT
Statistics
Matches: 226, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 226 1.00
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (55 bp):
ATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTACTTA
Found at i:27716 original size:15 final size:15
Alignment explanation
Indices: 27696--27724 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
27686 GCATGCGCTG
27696 AAAAATAAAAATAAT
1 AAAAATAAAAATAAT
27711 AAAAATAAAAATAA
1 AAAAATAAAAATAA
27725 ATGCTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATAAAAATAAT
Found at i:28700 original size:22 final size:22
Alignment explanation
Indices: 28675--28717 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
28665 GATGACTAAT
28675 TTAACAATGCACTTGAATTTGA
1 TTAACAATGCACTTGAATTTGA
28697 TTAACAATGCACTTGAATTTG
1 TTAACAATGCACTTGAATTTG
28718 TAATGAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (22 bp):
TTAACAATGCACTTGAATTTGA
Found at i:29306 original size:26 final size:26
Alignment explanation
Indices: 29277--29328 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
29267 TGCTTGCTTG
29277 ACAGCCCCTTGCATGTTCCTTGTTTC
1 ACAGCCCCTTGCATGTTCCTTGTTTC
29303 ACAGCCCCTTGCATGTTCCTTGTTTC
1 ACAGCCCCTTGCATGTTCCTTGTTTC
29329 CTTTAATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.12, C:0.35, G:0.15, T:0.38
Consensus pattern (26 bp):
ACAGCCCCTTGCATGTTCCTTGTTTC
Found at i:30007 original size:16 final size:16
Alignment explanation
Indices: 29986--30041 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
29976 TGTGACTGAA
29986 ATGCAAGAATATTGAG
1 ATGCAAGAATATTGAG
* * *
30002 ATGCAA-AAAAATGCCAAA
1 ATGCAAGAATATTG---AG
30020 ATGCAAGAATATTGAG
1 ATGCAAGAATATTGAG
30036 ATGCAA
1 ATGCAA
30042 AAAATGCCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
15 5 0.17
16 13 0.43
18 7 0.23
19 5 0.17
ACGTcount: A:0.50, C:0.11, G:0.20, T:0.20
Consensus pattern (16 bp):
ATGCAAGAATATTGAG
Found at i:30049 original size:33 final size:34
Alignment explanation
Indices: 29984--30053 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
29974 TATGTGACTG
29984 AAATGCAAGAATATTGAGATGCAAAAAAATGCCA
1 AAATGCAAGAATATTGAGATGCAAAAAAATGCCA
30018 AAATGCAAGAATATTGAGATGC-AAAAAATGCCA
1 AAATGCAAGAATATTGAGATGCAAAAAAATGCCA
30051 AAA
1 AAA
30054 GTACACATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 14 0.39
34 22 0.61
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (34 bp):
AAATGCAAGAATATTGAGATGCAAAAAAATGCCA
Done.