Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009995.1 Corchorus capsularis cultivar CVL-1 contig10016, 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: 10288
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Found at i:3362 original size:15 final size:15
Alignment explanation
Indices: 3342--3384 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
3332 AGTCCAAGTT
*
3342 GCTCATCTTCTTGTG
1 GCTCATCTTCTGGTG
3357 GCTCATCTTCTGGTG
1 GCTCATCTTCTGGTG
3372 GCTCATCTTCTGG
1 GCTCATCTTCTGG
3385 CTTAGTAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.07, C:0.28, G:0.23, T:0.42
Consensus pattern (15 bp):
GCTCATCTTCTGGTG
Found at i:4427 original size:17 final size:18
Alignment explanation
Indices: 4405--4444 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
4395 CCTAAATTTA
*
4405 TTTTCGA-CACAATTTTT
1 TTTTCGACCAAAATTTTT
4422 TTTTCGACGCAAAATTTTT
1 TTTTCGAC-CAAAATTTTT
4441 TTTT
1 TTTT
4445 ATAGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
19 13 0.65
ACGTcount: A:0.23, C:0.15, G:0.07, T:0.55
Consensus pattern (18 bp):
TTTTCGACCAAAATTTTT
Found at i:4774 original size:6 final size:6
Alignment explanation
Indices: 4758--4788 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
4748 CAAAGCAAAA
4758 TAAAT- TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TA
4789 TAGCAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:7257 original size:19 final size:18
Alignment explanation
Indices: 7233--7269 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
7223 ACCCCGAGTG
7233 CTTTTTCTTCTTCTTTTTT
1 CTTTTTCTTC-TCTTTTTT
7252 CTTTTTCTTCTCTTTTTT
1 CTTTTTCTTCTCTTTTTT
7270 ATTATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
CTTTTTCTTCTCTTTTTT
Found at i:7277 original size:9 final size:9
Alignment explanation
Indices: 7265--7298 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
7255 TTTCTTCTCT
7265 TTTTTATTA
1 TTTTTATTA
7274 -TTTTATTA
1 TTTTTATTA
*
7282 TTTTTTTTA
1 TTTTTATTA
7291 TTTTTATT
1 TTTTTATT
7299 TGGATGGGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTATTA
Found at i:7277 original size:20 final size:19
Alignment explanation
Indices: 7234--7295 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
7224 CCCCGAGTGC
*
7234 TTTTTCTTCTTCTTTTTT-C
1 TTTTTCTTC-TCTTTTTTAT
7253 TTTTTCTTCTCTTTTTTAT
1 TTTTTCTTCTCTTTTTTAT
* * *
7272 TATTTTATTATTTTTTTTAT
1 T-TTTTCTTCTCTTTTTTAT
7292 TTTT
1 TTTT
7296 ATTTGGATGG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.22
19 13 0.35
20 16 0.43
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTCTTCTCTTTTTTAT
Found at i:7576 original size:2 final size:2
Alignment explanation
Indices: 7569--7603 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
7559 GAACAACAAA
7569 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7604 CACAAAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.