Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015466.1 Corchorus capsularis cultivar CVL-1 contig15487, 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: 35577
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:39 original size:13 final size:12
Alignment explanation
Indices: 1--39 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
1 TATATATATATATA
1 TATAT-TATATA-A
15 TATATTATATAA
1 TATATTATATAA
27 TATGATTATATAA
1 TAT-ATTATATAA
40 ATGCATGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 4 0.17
13 15 0.62
14 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (12 bp):
TATATTATATAA
Found at i:3723 original size:12 final size:12
Alignment explanation
Indices: 3706--3753 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
3696 CCAAACTCAG
3706 CAGCAGACACAA
1 CAGCAGACACAA
*
3718 CAGCAGACACAG
1 CAGCAGACACAA
*
3730 CAGCAAACACAA
1 CAGCAGACACAA
* *
3742 CAACATACACAA
1 CAGCAGACACAA
3754 TCCAAAACAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.52, C:0.33, G:0.12, T:0.02
Consensus pattern (12 bp):
CAGCAGACACAA
Found at i:3739 original size:24 final size:24
Alignment explanation
Indices: 3703--3752 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
3693 GTCCCAAACT
* *
3703 CAGCAGCAGACACAACAGCAGACA
1 CAGCAGCAAACACAACAACAGACA
*
3727 CAGCAGCAAACACAACAACATACA
1 CAGCAGCAAACACAACAACAGACA
3751 CA
1 CA
3753 ATCCAAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.34, G:0.14, T:0.02
Consensus pattern (24 bp):
CAGCAGCAAACACAACAACAGACA
Found at i:5471 original size:2 final size:2
Alignment explanation
Indices: 5464--5494 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
5454 ATACACGAGA
5464 AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
5495 TATTTTTATC
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:5651 original size:11 final size:11
Alignment explanation
Indices: 5635--5677 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
5625 TATACTATAT
5635 CTAATTAATAG
1 CTAATTAATAG
*
5646 CTAATTAATAT
1 CTAATTAATAG
5657 CTAATTAATAG
1 CTAATTAATAG
*
5668 TTAATTAATA
1 CTAATTAATA
5678 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:5656 original size:22 final size:22
Alignment explanation
Indices: 5631--5677 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
5621 CCATTATACT
5631 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
5653 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
5675 ATA
1 ATA
5678 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:9446 original size:17 final size:16
Alignment explanation
Indices: 9411--9442 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9401 CCCAGAAATT
9411 CAAAAAAAAAAAAAGG
1 CAAAAAAAAAAAAAGG
*
9427 CAAAAGAAAAAAAAGG
1 CAAAAAAAAAAAAAGG
9443 GCAAGTGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (16 bp):
CAAAAAAAAAAAAAGG
Found at i:25242 original size:2 final size:2
Alignment explanation
Indices: 25235--25262 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25225 CAAACAAATA
25235 AT AT 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
25263 TTTAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31328 original size:7 final size:7
Alignment explanation
Indices: 31316--31344 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
31306 AAAAGCAGAA
31316 TGCACTT
1 TGCACTT
31323 TGCACTT
1 TGCACTT
31330 TGCACTT
1 TGCACTT
31337 TGCACTT
1 TGCACTT
31344 T
1 T
31345 TTACAAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (7 bp):
TGCACTT
Done.