Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012568.1 Corchorus capsularis cultivar CVL-1 contig12589, 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: 10918
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:5629 original size:22 final size:23
Alignment explanation
Indices: 5574--5637 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 23
5564 TTTGTTCATT
*
5574 TATATTATTATATATATTATATA
1 TATAATATTATATATATTATATA
*
5597 TATAATAATTATAT-T-TTATTTA
1 TATAAT-ATTATATATATTATATA
5619 TATAAATATTAATATATAT
1 TAT-AATATT-ATATATAT
5638 AATTATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 12 0.35
23 13 0.38
24 8 0.24
25 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATAATATTATATATATTATATA
Found at i:5638 original size:16 final size:15
Alignment explanation
Indices: 5616--5659 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 15
5606 TATATTTTAT
5616 TTATATAAATATTAA
1 TTATATAAATATTAA
*
5631 TATATATAATTATT--
1 T-TATATAAATATTAA
5645 TTATATAAATATTAA
1 TTATATAAATATTAA
5660 AAAATATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 11 0.46
14 1 0.04
15 1 0.04
16 11 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATATAAATATTAA
Found at i:5656 original size:29 final size:26
Alignment explanation
Indices: 5575--5659 Score: 95
Period size: 29 Copynumber: 3.3 Consensus size: 26
5565 TTGTTCATTT
*
5575 ATATT-ATTATATA-TA-TTATATAT
1 ATATTAATTATATATTATTTATATAA
* *
5598 ATAATAATTATATTTTATTTATATAA
1 ATATTAATTATATATTATTTATATAA
5624 ATATTAATATATATAATTATTTTATATAA
1 ATATTAAT-TATAT-ATTA-TTTATATAA
5653 ATATTAA
1 ATATTAA
5660 AAAATATATT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
23 4 0.08
24 7 0.14
25 2 0.04
26 14 0.27
27 5 0.10
28 3 0.06
29 16 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATATTAATTATATATTATTTATATAA
Found at i:6778 original size:21 final size:20
Alignment explanation
Indices: 6725--6778 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
6715 TTAGTAATTA
6725 TACAGATGAAATT-ATACTG
1 TACAGATGAAATTAATACTG
* * *
6744 TAAAGATTAGATTAAGTACTG
1 TACAGATGAAATTAA-TACTG
6765 TACAGATGAAATTA
1 TACAGATGAAATTA
6779 TTAGAGCAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 10 0.37
20 1 0.04
21 16 0.59
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.31
Consensus pattern (20 bp):
TACAGATGAAATTAATACTG
Found at i:7287 original size:15 final size:16
Alignment explanation
Indices: 7267--7296 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
7257 AGACAAGCAC
7267 AAAAAAGAA-AAGAAA
1 AAAAAAGAAGAAGAAA
7282 AAAAAAGAAGAAGAA
1 AAAAAAGAAGAAGAA
7297 CAGAGAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAGAAGAAA
Found at i:8376 original size:2 final size:2
Alignment explanation
Indices: 8371--8397 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8361 GGGGGGAAAA
8371 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
8398 TTAAACGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.