Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001292.1 Corchorus capsularis cultivar CVL-1 contig01292, 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: 9101
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:1870 original size:2 final size:2
Alignment explanation
Indices: 1830--1857 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1820 CAAATATAAA
1830 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
1858 GCTCAAAATA
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:3853 original size:6 final size:6
Alignment explanation
Indices: 3822--3851 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3812 GGTTCCATAT
*
3822 CTGGGA CTGGGA CTGGGA CTGGGA ATGGGA
1 CTGGGA CTGGGA CTGGGA CTGGGA CTGGGA
3852 ATAGAGAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.13, G:0.50, T:0.17
Consensus pattern (6 bp):
CTGGGA
Found at i:4268 original size:16 final size:16
Alignment explanation
Indices: 4247--4298 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
4237 ACCTGAATCT
4247 GAACCTGAAAAAACCC
1 GAACCTGAAAAAACCC
* *
4263 GAACCTGAAAAAATCA
1 GAACCTGAAAAAACCC
4279 GAACCTG-AAAAACCC
1 GAACCTGAAAAAACCC
4294 GAACC
1 GAACC
4299 CGAACTTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
15 11 0.34
16 21 0.66
ACGTcount: A:0.50, C:0.29, G:0.13, T:0.08
Consensus pattern (16 bp):
GAACCTGAAAAAACCC
Found at i:4515 original size:16 final size:16
Alignment explanation
Indices: 4494--4581 Score: 72
Period size: 16 Copynumber: 5.5 Consensus size: 16
4484 CCCGAATCCG
*
4494 AATTAACCTGACCCAA
1 AATTAACCCGACCCAA
*
4510 AATTAACCCGAACCC-G
1 AATTAACCCG-ACCCAA
*
4526 AATCAACCCGACCCAA
1 AATTAACCCGACCCAA
* * *
4542 ATTTAACCCGAATCC-G
1 AATTAACCCG-ACCCAA
*
4558 AATCAACCCGACCCAA
1 AATTAACCCGACCCAA
*
4574 ATTTAACC
1 AATTAACC
4582 TGAACCTGGA
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
15 7 0.13
16 40 0.74
17 7 0.13
ACGTcount: A:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (16 bp):
AATTAACCCGACCCAA
Found at i:4520 original size:32 final size:32
Alignment explanation
Indices: 4484--4581 Score: 160
Period size: 32 Copynumber: 3.1 Consensus size: 32
4474 CCAATCCGAG
* * *
4484 CCCGAATCCGAATTAACCTGACCCAAAATTAA
1 CCCGAATCCGAATCAACCCGACCCAAATTTAA
*
4516 CCCGAACCCGAATCAACCCGACCCAAATTTAA
1 CCCGAATCCGAATCAACCCGACCCAAATTTAA
4548 CCCGAATCCGAATCAACCCGACCCAAATTTAA
1 CCCGAATCCGAATCAACCCGACCCAAATTTAA
4580 CC
1 CC
4582 TGAACCTGGA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.38, C:0.38, G:0.09, T:0.15
Consensus pattern (32 bp):
CCCGAATCCGAATCAACCCGACCCAAATTTAA
Found at i:4979 original size:23 final size:23
Alignment explanation
Indices: 4933--4979 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
4923 GAAGCATAAA
*
4933 ATTTCATAAAAGATTAATAGTTT
1 ATTTCATAAAAGATTAATAATTT
*
4956 ATTTCATTAAAA-ATTTATAATTT
1 ATTTCA-TAAAAGATTAATAATTT
4979 A
1 A
4980 CAAATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (23 bp):
ATTTCATAAAAGATTAATAATTT
Found at i:5037 original size:23 final size:23
Alignment explanation
Indices: 4992--5038 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
4982 AATTATAAAT
*
4992 AAAAAATAATTAAATATAATACA
1 AAAAAATAATTAAATAGAATACA
*
5015 AAAAAAT-ATTACATAGAACTACA
1 AAAAAATAATTAAATAGAA-TACA
5038 A
1 A
5039 CTTTACTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (23 bp):
AAAAAATAATTAAATAGAATACA
Found at i:5077 original size:23 final size:26
Alignment explanation
Indices: 5020--5078 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
5010 ATACAAAAAA
*
5020 ATATTACATAGAACTACAACTTTACT
1 ATATTACATAGAACAACAACTTTACT
* *
5046 TTATTACATAGAA-AAGAAC-TTAC-
1 ATATTACATAGAACAACAACTTTACT
5069 ATATTACATA
1 ATATTACATA
5079 TATGTAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 9 0.31
24 4 0.14
25 4 0.14
26 12 0.41
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (26 bp):
ATATTACATAGAACAACAACTTTACT
Found at i:6709 original size:29 final size:30
Alignment explanation
Indices: 6637--6723 Score: 108
Period size: 30 Copynumber: 2.9 Consensus size: 30
6627 TGGACAAGAG
*
6637 GAAATATAATAATTAC-TTTAGATTGATTGT
1 GAAATATATTAATTACTTTTA-ATTGATTGT
6667 GAAATATATTAATTACTTTTAATTGATTG-
1 GAAATATATTAATTACTTTTAATTGATTGT
* *
6696 GAAA-ATATTTAATTATTTTTGATTGATT
1 GAAATATA-TTAATTACTTTTAATTGATT
6724 AATTAGTTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
28 3 0.06
29 22 0.42
30 23 0.44
31 4 0.08
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.48
Consensus pattern (30 bp):
GAAATATATTAATTACTTTTAATTGATTGT
Found at i:9014 original size:16 final size:16
Alignment explanation
Indices: 8976--9007 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8966 TAATTGATAG
*
8976 TTGAGTTAATTTCTAA
1 TTGAGTTAATTACTAA
8992 TTGAGTTAATTACTAA
1 TTGAGTTAATTACTAA
9008 ATTAGTTTCT
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:0.34, C:0.06, G:0.12, T:0.47
Consensus pattern (16 bp):
TTGAGTTAATTACTAA
Done.