Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007729.1 Corchorus capsularis cultivar CVL-1 contig07750, 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: 21820
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2881 original size:2 final size:2
Alignment explanation
Indices: 2876--2900 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2866 TCATATGAAT
2876 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2901 TTGCAAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6190 original size:75 final size:75
Alignment explanation
Indices: 6101--6249 Score: 280
Period size: 75 Copynumber: 2.0 Consensus size: 75
6091 TGTTTAACTA
*
6101 CGGTTTGCACTTATGAAGCCAACCCACTAGGCACTCGTAGGCGTATTACAAGATTGTCTAATCCT
1 CGGTTTGCACTTATGAAGCCAACCCACTAGGCACTCGTAGGCGTATAACAAGATTGTCTAATCCT
6166 ATTAAGTTTG
66 ATTAAGTTTG
*
6176 CGGTTTGCACTTATGAAGCCAACCCACTAGGCACTCGTAGGCGTATAACAAGATTGTCTAATCTT
1 CGGTTTGCACTTATGAAGCCAACCCACTAGGCACTCGTAGGCGTATAACAAGATTGTCTAATCCT
6241 ATTAAGTTT
66 ATTAAGTTT
6250 TCTGCAGCAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (75 bp):
CGGTTTGCACTTATGAAGCCAACCCACTAGGCACTCGTAGGCGTATAACAAGATTGTCTAATCCT
ATTAAGTTTG
Found at i:7277 original size:19 final size:19
Alignment explanation
Indices: 7249--7291 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
7239 AATTAATTGT
7249 TTTAATATTA-AATTTTTA
1 TTTAATATTATAATTTTTA
7267 TTTATATATTATAATTTTTA
1 TTTA-ATATTATAATTTTTA
*
7287 CTTAA
1 TTTAA
7292 AAATTACTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 7 0.32
20 11 0.50
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAATATTATAATTTTTA
Found at i:7297 original size:20 final size:19
Alignment explanation
Indices: 7255--7297 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
7245 TTGTTTTAAT
* * *
7255 ATTAAATTTTTATTTATAT
1 ATTAAATTTTTACTTAAAA
7274 ATTATAATTTTTACTTAAAA
1 ATTA-AATTTTTACTTAAAA
7294 ATTA
1 ATTA
7298 CTCATAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTAAATTTTTACTTAAAA
Found at i:12387 original size:16 final size:16
Alignment explanation
Indices: 12368--12404 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
12358 TATTTAAAAA
* *
12368 AAAAATATTTTTTTTT
1 AAAAATATATTCTTTT
12384 AAAAATATATTCTTTT
1 AAAAATATATTCTTTT
12400 AAAAA
1 AAAAA
12405 AAAATTGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAAATATATTCTTTT
Found at i:12543 original size:2 final size:2
Alignment explanation
Indices: 12536--12565 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12526 TATGTAGTAA
12536 AT 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 AT
12566 GAAATTGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17014 original size:32 final size:32
Alignment explanation
Indices: 16975--17081 Score: 151
Period size: 32 Copynumber: 3.3 Consensus size: 32
16965 CGGGCTTAAG
* *
16975 TCGGGTTCGGGTTAAAGTTGGGTCGGGTTGAT
1 TCGGGTTCGGGTTAAATTTGGGTCAGGTTGAT
*
17007 TCGGGTTCGGATTAAATTTGGGTCAGGTTGAT
1 TCGGGTTCGGGTTAAATTTGGGTCAGGTTGAT
* * * *
17039 TCAGGTTCGGGTCAATTTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTAAATTTGGGTCAGGTTGAT
17071 TCGGGTTCGGG
1 TCGGGTTCGGG
17082 CTCGGATTGG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.15, C:0.11, G:0.38, T:0.36
Consensus pattern (32 bp):
TCGGGTTCGGGTTAAATTTGGGTCAGGTTGAT
Found at i:17016 original size:16 final size:16
Alignment explanation
Indices: 16961--17081 Score: 79
Period size: 16 Copynumber: 7.5 Consensus size: 16
16951 GCCGTTTTCA
*
16961 GGTTCGGGCTTAAGTCG
1 GGTTCGGG-TTAATTCG
16978 GGTTCGGGTTAAAGTT-G
1 GGTTCGGGTT-AA-TTCG
*
16995 GG-TCGGGTTGATTCG
1 GGTTCGGGTTAATTCG
* *
17010 GGTTCGGATTAAATTTG
1 GGTTCGGGTT-AATTCG
* * *
17027 GG-TCAGGTTGATTCA
1 GGTTCGGGTTAATTCG
* *
17042 GGTTCGGGTCAATTTTG
1 GGTTCGGGTTAA-TTCG
*
17059 GG-TCAGGTTAATTCG
1 GGTTCGGGTTAATTCG
17074 GGTTCGGG
1 GGTTCGGG
17082 CTCGGATTGG
Statistics
Matches: 77, Mismatches: 19, Indels: 17
0.68 0.17 0.15
Matches are distributed among these distances:
14 2 0.03
15 14 0.18
16 37 0.48
17 23 0.30
18 1 0.01
ACGTcount: A:0.15, C:0.12, G:0.39, T:0.35
Consensus pattern (16 bp):
GGTTCGGGTTAATTCG
Found at i:17318 original size:16 final size:16
Alignment explanation
Indices: 17271--17332 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
17261 TGAATTCAGG
17271 TTCGGGTTC-GGTTTT
1 TTCGGGTTCGGGTTTT
* * *
17286 TTCGGGTTTGAGCTTT
1 TTCGGGTTCGGGTTTT
*
17302 TTCGAGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
*
17318 TTTGGGTTCGGGTTT
1 TTCGGGTTCGGGTTT
17333 GGGCGGGTTC
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
15 8 0.22
16 29 0.78
ACGTcount: A:0.03, C:0.11, G:0.34, T:0.52
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:21528 original size:9 final size:9
Alignment explanation
Indices: 21490--21527 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
21480 TCTATGATGA
21490 GGGCACTTG
1 GGGCACTTG
21499 GGGCACTTG
1 GGGCACTTG
21508 GGGCACTT-
1 GGGCACTTG
21516 GGGCATCTTG
1 GGGCA-CTTG
21526 GG
1 GG
21528 CCTTGATGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 5 0.19
9 20 0.74
10 2 0.07
ACGTcount: A:0.11, C:0.21, G:0.45, T:0.24
Consensus pattern (9 bp):
GGGCACTTG
Done.