Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010362.1 Corchorus capsularis cultivar CVL-1 contig10383, 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: 29384
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6875 original size:17 final size:17
Alignment explanation
Indices: 6853--6887 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6843 GCTTAATTTG
6853 TTCTTTTCTTTT-TCTTT
1 TTCTTTT-TTTTCTCTTT
6870 TTCTTTTTTTTCTCTTT
1 TTCTTTTTTTTCTCTTT
6887 T
1 T
6888 AACAACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTCTTTTTTTTCTCTTT
Found at i:11539 original size:53 final size:53
Alignment explanation
Indices: 11458--11564 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 53
11448 TTGTTATTAT
* *
11458 TTCACAACAAAATTTGATTTCTTGACTGAATTTTCTTAAGAGAATTTAAAAAA
1 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTAAAAAA
* *
11511 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAATAATTTATAAAA
1 TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTAAAAAA
11564 T
1 T
11565 AAAACAGCCG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (53 bp):
TTCACAACAAAATTTGATTTCTTAACTGAATTTTCTTAAAAGAATTTAAAAAA
Found at i:13349 original size:17 final size:17
Alignment explanation
Indices: 13327--13367 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 17
13317 GAAATTATTA
13327 GACAACTTCATCCAATT
1 GACAACTTCATCCAATT
13344 GACAA---C-TCCAATT
1 GACAACTTCATCCAATT
13357 GACAACTTCAT
1 GACAACTTCAT
13368 TCTTAAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 8
0.71 0.00 0.29
Matches are distributed among these distances:
13 12 0.60
14 1 0.05
16 1 0.05
17 6 0.30
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (17 bp):
GACAACTTCATCCAATT
Found at i:21151 original size:32 final size:32
Alignment explanation
Indices: 21095--21212 Score: 166
Period size: 32 Copynumber: 3.7 Consensus size: 32
21085 CGGGCTTGAG
21095 TCGGGTTCGGGTT-AATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTCAATTTGGGTCAGGTTAAT
** *
21126 TCGGGTTCGGGTTCTGTTTGGGTCAGATTAAT
1 TCGGGTTCGGGTTCAATTTGGGTCAGGTTAAT
* *
21158 TCGGGTTCGGGTTGAATTTGGGTCATGTTAAT
1 TCGGGTTCGGGTTCAATTTGGGTCAGGTTAAT
**
21190 TCGGGTTCGGGTTCTGTTTGGGT
1 TCGGGTTCGGGTTCAATTTGGGT
21213 TTTGGCCAGA
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
31 13 0.17
32 62 0.83
ACGTcount: A:0.12, C:0.11, G:0.36, T:0.41
Consensus pattern (32 bp):
TCGGGTTCGGGTTCAATTTGGGTCAGGTTAAT
Found at i:21393 original size:32 final size:32
Alignment explanation
Indices: 21351--21451 Score: 139
Period size: 32 Copynumber: 3.1 Consensus size: 32
21341 TTTTCATAAA
*
21351 TTTTCAGATTCGGGTTTTTTCGGGTTTGAGCT
1 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCT
*
21383 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGTT
1 TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCT
* * * *
21415 TTTTCGGGTTTGTGTTTTTTTCGGGTTTGAACT
1 TTTTCGGATTCG-GGTTTTTTCGGGTTTGAGCT
21448 TTTT
1 TTTT
21452 TCGGGTTCAG
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
32 40 0.66
33 21 0.34
ACGTcount: A:0.07, C:0.10, G:0.28, T:0.55
Consensus pattern (32 bp):
TTTTCGGATTCGGGTTTTTTCGGGTTTGAGCT
Found at i:21439 original size:17 final size:16
Alignment explanation
Indices: 21364--21458 Score: 118
Period size: 16 Copynumber: 5.8 Consensus size: 16
21354 TCAGATTCGG
21364 GTTTTTTCGGGTTTGA
1 GTTTTTTCGGGTTTGA
* * * *
21380 GCTTTTTCGGATTCGG
1 GTTTTTTCGGGTTTGA
21396 GTTTTTTCGGGTTTGA
1 GTTTTTTCGGGTTTGA
*
21412 GTTTTTTCGGGTTTGT
1 GTTTTTTCGGGTTTGA
21428 GTTTTTTTCGGGTTTGAA
1 G-TTTTTTCGGGTTTG-A
*
21446 CTTTTTTCGGGTT
1 GTTTTTTCGGGTT
21459 CAGGTTCAGG
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
16 40 0.61
17 26 0.39
ACGTcount: A:0.05, C:0.09, G:0.29, T:0.56
Consensus pattern (16 bp):
GTTTTTTCGGGTTTGA
Found at i:26598 original size:21 final size:21
Alignment explanation
Indices: 26572--26620 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
26562 TTTAGGTTGG
26572 TTCCTAGCACAAATTGTAAAC
1 TTCCTAGCACAAATTGTAAAC
26593 TTCCTAGCACAAATTGTAAAC
1 TTCCTAGCACAAATTGTAAAC
26614 TTCCTAG
1 TTCCTAG
26621 ACTTTTGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.31
Consensus pattern (21 bp):
TTCCTAGCACAAATTGTAAAC
Found at i:29356 original size:2 final size:2
Alignment explanation
Indices: 29349--29378 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29339 AAGGTCTTGT
29349 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
29379 ATTCTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Done.