Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013658.1 Corchorus capsularis cultivar CVL-1 contig13679, 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: 71648
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:121 original size:17 final size:17
Alignment explanation
Indices: 99--135 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
89 CTAGGATGAA
*
99 TAAATGGAAAAATTGGT
1 TAAATGAAAAAATTGGT
116 TAAATGAAAAAATTGGT
1 TAAATGAAAAAATTGGT
133 TAA
1 TAA
136 GAGGTCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (17 bp):
TAAATGAAAAAATTGGT
Found at i:591 original size:21 final size:21
Alignment explanation
Indices: 567--608 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
557 CACTTTATAG
567 TATTAAAAATAAAAACAAAAA
1 TATTAAAAATAAAAACAAAAA
* *
588 TATTAGAAATAAAAATAAAAA
1 TATTAAAAATAAAAACAAAAA
609 CGCTTTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (21 bp):
TATTAAAAATAAAAACAAAAA
Found at i:859 original size:17 final size:17
Alignment explanation
Indices: 837--873 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
827 CTAGGATGAA
*
837 TAAATGGAAAAATTGGT
1 TAAATGAAAAAATTGGT
854 TAAATGAAAAAATTGGT
1 TAAATGAAAAAATTGGT
871 TAA
1 TAA
874 GAGGTCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (17 bp):
TAAATGAAAAAATTGGT
Found at i:16740 original size:48 final size:48
Alignment explanation
Indices: 16669--16761 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
16659 ACATTGAGAG
16669 TAAGTTAGGTAAATGTGCTAGATATGTATAATTTTTGAGCTTAAATAA
1 TAAGTTAGGTAAATGTGCTAGATATGTATAATTTTTGAGCTTAAATAA
* * * *
16717 TAAGTTGGGTAGATGTGTTAGATATGTATAGTTTTTGAGCTTAAA
1 TAAGTTAGGTAAATGTGCTAGATATGTATAATTTTTGAGCTTAAA
16762 AAGAATTGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.33, C:0.03, G:0.23, T:0.41
Consensus pattern (48 bp):
TAAGTTAGGTAAATGTGCTAGATATGTATAATTTTTGAGCTTAAATAA
Found at i:20195 original size:2 final size:2
Alignment explanation
Indices: 20190--20218 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20180 GTACCAAAGA
20190 AG 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 AG A
20219 AGAAAACTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33980 original size:13 final size:13
Alignment explanation
Indices: 33962--34000 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
33952 ATAACGTGAA
33962 GTCCTGAGTTTAT
1 GTCCTGAGTTTAT
33975 GTCCTGAGTTTAT
1 GTCCTGAGTTTAT
33988 GTCAC-GAGTTTAT
1 GTC-CTGAGTTTAT
34001 TCGGATACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 24 0.96
14 1 0.04
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.44
Consensus pattern (13 bp):
GTCCTGAGTTTAT
Found at i:42605 original size:6 final size:6
Alignment explanation
Indices: 42594--42627 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
42584 AAGCTAGTTC
42594 GTAGCG GTAGCG GTAGCG GTAGCG GTAGCG GTAG
1 GTAGCG GTAGCG GTAGCG GTAGCG GTAGCG GTAG
42628 GGGGTTCACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.15, G:0.50, T:0.18
Consensus pattern (6 bp):
GTAGCG
Found at i:44279 original size:14 final size:14
Alignment explanation
Indices: 44262--44294 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
44252 TCTACTAGTA
44262 ATATATATGTAGCC
1 ATATATATGTAGCC
44276 ATATATATGTAGCC
1 ATATATATGTAGCC
*
44290 GTATA
1 ATATA
44295 GTACTGCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (14 bp):
ATATATATGTAGCC
Found at i:46394 original size:22 final size:22
Alignment explanation
Indices: 46369--46416 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
46359 TTATTGCACC
*
46369 ATTACAAGGTGTTATAGAAAAG
1 ATTACAAGGTGTAATAGAAAAG
*
46391 ATTACAAGGTGTAATAGAAAGG
1 ATTACAAGGTGTAATAGAAAAG
46413 ATTA
1 ATTA
46417 TACATTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.23, T:0.27
Consensus pattern (22 bp):
ATTACAAGGTGTAATAGAAAAG
Found at i:49472 original size:30 final size:30
Alignment explanation
Indices: 49438--49500 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
49428 TCGGTAAGAA
*
49438 AAACGACAGAGGAAACGATGGCAACGCTTC
1 AAACGACAGAGGAAACGACGGCAACGCTTC
*
49468 AAACGGCAGAGGAAACGACGGCAACGCTTC
1 AAACGACAGAGGAAACGACGGCAACGCTTC
49498 AAA
1 AAA
49501 TCTCGGCCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.24, G:0.27, T:0.08
Consensus pattern (30 bp):
AAACGACAGAGGAAACGACGGCAACGCTTC
Found at i:51677 original size:63 final size:63
Alignment explanation
Indices: 51593--51718 Score: 207
Period size: 63 Copynumber: 2.0 Consensus size: 63
51583 AATTACGATC
* *
51593 TGGATTCGACTGTAATGTATGATGAAGTCGGAATCGGAACCGGAAGGGCGGTGCAGGAATCTG
1 TGGATTCAACTGAAATGTATGATGAAGTCGGAATCGGAACCGGAAGGGCGGTGCAGGAATCTG
* * *
51656 TGGATTCAACTGAAATTTATGATGAAGTCGGAATCGGAATCGGAAGGGCGGTGGAGGAATCTG
1 TGGATTCAACTGAAATGTATGATGAAGTCGGAATCGGAACCGGAAGGGCGGTGCAGGAATCTG
51719 CATTAGAGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.29, C:0.13, G:0.36, T:0.23
Consensus pattern (63 bp):
TGGATTCAACTGAAATGTATGATGAAGTCGGAATCGGAACCGGAAGGGCGGTGCAGGAATCTG
Done.