Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006909.1 Corchorus capsularis cultivar CVL-1 contig06930, 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: 24223
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:3513 original size:24 final size:24
Alignment explanation
Indices: 3459--3515 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
3449 ATACATAACT
*
3459 ACGACCACGACCGCGACCATAGCC
1 ACGACCACGACCACGACCATAGCC
** *
3483 AAAACCACGACCACGTCCAT-GTCC
1 ACGACCACGACCACGACCATAG-CC
3507 ACGACCACG
1 ACGACCACG
3516 TCCATAATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.32, C:0.44, G:0.18, T:0.07
Consensus pattern (24 bp):
ACGACCACGACCACGACCATAGCC
Found at i:4499 original size:33 final size:33
Alignment explanation
Indices: 4459--4527 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
4449 TTTAATAATA
*
4459 AAAGAAAGGTAGAAGAAGGAAATTATGCATGAT
1 AAAGAAAGGTAGAAGAAGGAAATCATGCATGAT
* *
4492 AAAGAAAGGTAGAAGAAGGAGATCATGTATGAT
1 AAAGAAAGGTAGAAGAAGGAAATCATGCATGAT
4525 AAA
1 AAA
4528 TAAACTTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.52, C:0.03, G:0.28, T:0.17
Consensus pattern (33 bp):
AAAGAAAGGTAGAAGAAGGAAATCATGCATGAT
Found at i:7953 original size:60 final size:60
Alignment explanation
Indices: 7889--8037 Score: 298
Period size: 60 Copynumber: 2.5 Consensus size: 60
7879 CCACCCATCC
7889 ATTTTAGTAATAAATAATAGTTCAATATTATGACAATAACTAGTTCCATATGTTAAATTA
1 ATTTTAGTAATAAATAATAGTTCAATATTATGACAATAACTAGTTCCATATGTTAAATTA
7949 ATTTTAGTAATAAATAATAGTTCAATATTATGACAATAACTAGTTCCATATGTTAAATTA
1 ATTTTAGTAATAAATAATAGTTCAATATTATGACAATAACTAGTTCCATATGTTAAATTA
8009 ATTTTAGTAATAAATAATAGTTCAATATT
1 ATTTTAGTAATAAATAATAGTTCAATATT
8038 TACCGCCCAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 89 1.00
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (60 bp):
ATTTTAGTAATAAATAATAGTTCAATATTATGACAATAACTAGTTCCATATGTTAAATTA
Found at i:9177 original size:64 final size:64
Alignment explanation
Indices: 9076--9197 Score: 226
Period size: 64 Copynumber: 1.9 Consensus size: 64
9066 CCACTCCTAA
*
9076 CAAAAAGAAAAGGTTTGTTATGTTGTAACCCCCAATTTGAATTCACATTTATTATATAGCCAAG
1 CAAAAAGAAAAAGTTTGTTATGTTGTAACCCCCAATTTGAATTCACATTTATTATATAGCCAAG
*
9140 CAAAAAGAAAAAGTTTGTTATGTTGTAACCCCCAATTTGAATTGACATTTATTATATA
1 CAAAAAGAAAAAGTTTGTTATGTTGTAACCCCCAATTTGAATTCACATTTATTATATA
9198 TTCAAGAAAG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (64 bp):
CAAAAAGAAAAAGTTTGTTATGTTGTAACCCCCAATTTGAATTCACATTTATTATATAGCCAAG
Found at i:15693 original size:25 final size:24
Alignment explanation
Indices: 15655--15706 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
15645 CAATAGAAAC
*
15655 TCAAATCAAGTTGTATCACTCGAGT
1 TCAAATCAACTTGTATCACTC-AGT
* *
15680 TCAAGTCAACTTGTATCATTCAGT
1 TCAAATCAACTTGTATCACTCAGT
15704 TCA
1 TCA
15707 GTTCATATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (24 bp):
TCAAATCAACTTGTATCACTCAGT
Found at i:17335 original size:6 final size:6
Alignment explanation
Indices: 17326--17365 Score: 71
Period size: 6 Copynumber: 6.5 Consensus size: 6
17316 AAAGCAAAAC
17326 AAATCT AAATCT AAATCT AAATCT AAATCT AAAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT -AAATCT AAA
17366 GCAAATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:17371 original size:18 final size:18
Alignment explanation
Indices: 17330--17371 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
17320 CAAAACAAAT
*
17330 CTAAATCTAAATCTAAAT
1 CTAAATCTAAATCTAAAG
17348 CTAAATCTAAAATCTAAAG
1 CTAAATCT-AAATCTAAAG
17367 C-AAAT
1 CTAAAT
17372 TAATAAAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (18 bp):
CTAAATCTAAATCTAAAG
Found at i:23963 original size:34 final size:33
Alignment explanation
Indices: 23920--23997 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 33
23910 ATAAAATTAA
*
23920 AAAGCAAAAACAGAAAATA-AAAATATATTTTTTT
1 AAAGGAAAAACAGAAAA-AGAAAAT-TATTTTTTT
*
23954 AAAGGAAAAACGGAAAAAGGAAAATTATTTTTTT
1 AAAGGAAAAACAGAAAAA-GAAAATTATTTTTTT
*
23988 AAAAGAAAAA
1 AAAGGAAAAA
23998 TCGAAAACCC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
33 1 0.03
34 33 0.85
35 5 0.13
ACGTcount: A:0.60, C:0.04, G:0.12, T:0.24
Consensus pattern (33 bp):
AAAGGAAAAACAGAAAAAGAAAATTATTTTTTT
Done.