Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014796.1 Corchorus capsularis cultivar CVL-1 contig14817, 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: 13432
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:2697 original size:24 final size:24
Alignment explanation
Indices: 2670--2716 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2660 AGTTATTCAG
2670 TTTATGTTT-TATCTTTAATTTTCT
1 TTTAT-TTTATATCTTTAATTTTCT
* *
2694 TTTATTTTATGTCTTTATTTTTC
1 TTTATTTTATATCTTTAATTTTC
2717 AAGTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.72
Consensus pattern (24 bp):
TTTATTTTATATCTTTAATTTTCT
Found at i:4570 original size:16 final size:16
Alignment explanation
Indices: 4534--4623 Score: 123
Period size: 16 Copynumber: 5.8 Consensus size: 16
4524 ATTGGGCGGG
* *
4534 TTCGGGTTCAGGTA-C
1 TTCGGGTTCGGGTATT
4549 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
4565 TTCGGGTTCGAG-ATTT
1 TTCGGGTTCGGGTA-TT
4581 TTCGGGTTCGGGTA-T
1 TTCGGGTTCGGGTATT
4596 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
4612 TTCGGGTTCGGG
1 TTCGGGTTCGGG
4624 CTCGGATCGG
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
15 29 0.43
16 37 0.55
17 1 0.01
ACGTcount: A:0.08, C:0.14, G:0.38, T:0.40
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:4590 original size:6 final size:6
Alignment explanation
Indices: 4581--4666 Score: 68
Period size: 6 Copynumber: 13.5 Consensus size: 6
4571 TTCGAGATTT
*
4581 TTCGGG TTCGGG TATTTCGGG TTCGGG TATTTTCGGG TTCGGG CTC-GG
1 TTCGGG TTCGGG ---TTCGGG TTCGGG ---T-TCGGG TTCGGG TTCGGG
* *
4629 ATCGGG TTCGGG TTCGGG TCCGGG -TCGGG TTCGGG TTC
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTC
4667 ACTTTCGATA
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
5 8 0.12
6 45 0.68
7 1 0.02
9 7 0.11
10 5 0.08
ACGTcount: A:0.03, C:0.19, G:0.44, T:0.34
Consensus pattern (6 bp):
TTCGGG
Found at i:4642 original size:23 final size:23
Alignment explanation
Indices: 4612--4666 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
4602 TTCGGGTATT
4612 TTCGGGTTCGGG-CTCGGATCGGG
1 TTCGGGTTCGGGTC-CGGATCGGG
*
4635 TTCGGGTTCGGGTCCGGGTCGGG
1 TTCGGGTTCGGGTCCGGATCGGG
4658 TTCGGGTTC
1 TTCGGGTTC
4667 ACTTTCGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.02, C:0.22, G:0.47, T:0.29
Consensus pattern (23 bp):
TTCGGGTTCGGGTCCGGATCGGG
Found at i:4656 original size:17 final size:18
Alignment explanation
Indices: 4614--4664 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
4604 CGGGTATTTT
* *
4614 CGGGTTCGGGCTCGGAT-
1 CGGGTTCGGGTTCGGGTC
4631 CGGGTTCGGGTTCGGGTC
1 CGGGTTCGGGTTCGGGTC
4649 CGGG-TCGGGTTCGGGT
1 CGGGTTCGGGTTCGGGT
4665 TCACTTTCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 27 0.87
18 4 0.13
ACGTcount: A:0.02, C:0.22, G:0.51, T:0.25
Consensus pattern (18 bp):
CGGGTTCGGGTTCGGGTC
Found at i:5422 original size:6 final size:6
Alignment explanation
Indices: 5412--5447 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
5402 TATTTTGATC
*
5412 TCGGGC TCGGG- TCGGGT TCGGGT TCGGGT TCGGGT T
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT T
5448 GTCTCAGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.00, C:0.19, G:0.50, T:0.31
Consensus pattern (6 bp):
TCGGGT
Found at i:5426 original size:11 final size:11
Alignment explanation
Indices: 5412--5446 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
5402 TATTTTGATC
*
5412 TCGGGCTCGGG
1 TCGGGTTCGGG
5423 TCGGGTTCGGG
1 TCGGGTTCGGG
5434 TTCGGGTTCGGG
1 -TCGGGTTCGGG
5446 T
1 T
5447 TGTCTCAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.00, C:0.20, G:0.51, T:0.29
Consensus pattern (11 bp):
TCGGGTTCGGG
Found at i:5459 original size:16 final size:16
Alignment explanation
Indices: 5438--5479 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
5428 TTCGGGTTCG
*
5438 GGTTCGGGTTGTCTCA
1 GGTTCGGGTTATCTCA
* *
5454 GGTTCGGGTAATTTCA
1 GGTTCGGGTTATCTCA
5470 GGTTCGGGTT
1 GGTTCGGGTT
5480 CGGGCGGGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.10, C:0.14, G:0.38, T:0.38
Consensus pattern (16 bp):
GGTTCGGGTTATCTCA
Found at i:6640 original size:15 final size:16
Alignment explanation
Indices: 6620--6653 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6610 AATTGCTTTC
*
6620 TTAGTTA-ATTTACTT
1 TTAGTTAGATTTAATT
6635 TTAGTTAGATTTAATT
1 TTAGTTAGATTTAATT
6651 TTA
1 TTA
6654 ATTCTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59
Consensus pattern (16 bp):
TTAGTTAGATTTAATT
Found at i:13405 original size:12 final size:13
Alignment explanation
Indices: 13380--13413 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
13370 ATAATTATTG
13380 TTTGCTTTATTAA
1 TTTGCTTTATTAA
13393 TTTGCTTTA-TAA
1 TTTGCTTTATTAA
*
13405 TCTGCTTTA
1 TTTGCTTTA
13414 GATTTAGATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTGCTTTATTAA
Done.