Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011628.1 Corchorus capsularis cultivar CVL-1 contig11649, 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: 22570
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:4215 original size:14 final size:14
Alignment explanation
Indices: 4196--4222 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4186 CTCCGCTTAA
4196 ACTTAATTACCCTT
1 ACTTAATTACCCTT
4210 ACTTAATTACCCT
1 ACTTAATTACCCT
4223 GAATTAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (14 bp):
ACTTAATTACCCTT
Found at i:4249 original size:35 final size:35
Alignment explanation
Indices: 4207--4823 Score: 972
Period size: 35 Copynumber: 17.7 Consensus size: 35
4197 CTTAATTACC
*
4207 CTTACTTAATTACCCTGAATTAAGTTGATTACTGC
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
4242 CTCACTTAATTACCCTAAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* * *
4277 ATTACTTAATTACCCTTAATTAAGTTTATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
4312 CTGACTTAATTACCCTGAATTAAGTTGATTATTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
4347 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
4382 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
4417 CTCACTTAATTACCCTGAATTAAGTTGATTATTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
4452 ATTACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
4487 CTCACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
4522 CTCACTTAATTACCCTGAATTAAGTAGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
4557 CTCACTTAATTACCCTGAATTAAGTTGATTATTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
4592 ATTACTTAATTACCCTGAATTAAGTTAATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
4627 CTCACTTAATTACCCTGAATTAAGTTGATTATTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
4662 ATTACTTAATTACCCTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
4697 CTCACTTAATTACCTTGAATTAAGTTGATTACTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
*
4732 CTTACTTAATTACCCTGAATTAAGTTGATTATTGA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
* *
4767 ATTACTTAATTACCCTGAATTAA---G-TTACTAA
1 CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
4798 CTTACTTAATTACCCTGAATTAAGTT
1 CTTACTTAATTACCCTGAATTAAGTT
4824 ACTTATTACT
Statistics
Matches: 534, Mismatches: 45, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
31 27 0.05
32 1 0.00
35 506 0.95
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.40
Consensus pattern (35 bp):
CTTACTTAATTACCCTGAATTAAGTTGATTACTGA
Found at i:5514 original size:50 final size:51
Alignment explanation
Indices: 5433--5582 Score: 171
Period size: 50 Copynumber: 2.9 Consensus size: 51
5423 CCTTCTAAAC
* * * * *
5433 TCAAATATGTATCACTTTTATTTACCGATTAATCACAAGTTCAATCTTTGA-
1 TCAAAAATGT-TCATTTTTATTTACCAATTAATCACAAATTCCATCTTTGAG
* * *
5484 TCCAAAAAT-TTCATTTTTATTCACCAATTAATCACAAATTCCATTTTTTAG
1 T-CAAAAATGTTCATTTTTATTTACCAATTAATCACAAATTCCATCTTTGAG
*
5535 TCAAAAGTGTTCATTTTTATTTA-CAAGTTAATCACAAATTCCATCTTT
1 TCAAAAATGTTCATTTTTATTTACCAA-TTAATCACAAATTCCATCTTT
5583 CACTTAAAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
50 42 0.50
51 36 0.43
52 6 0.07
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (51 bp):
TCAAAAATGTTCATTTTTATTTACCAATTAATCACAAATTCCATCTTTGAG
Found at i:5592 original size:101 final size:102
Alignment explanation
Indices: 5448--5636 Score: 217
Period size: 101 Copynumber: 1.9 Consensus size: 102
5438 TATGTATCAC
* * * * * *
5448 TTTTATTTACCGATTAATCACAAGTTCAATCTTTGATCC-AAAAATTTCA-TTTTTATTCACCAA
1 TTTTATTTACAGATTAATCACAAATTCAATCTTTCATCCAAAAAAATCCACTCTTTATT-A-CAA
* *
5511 -TTAATCACAAATTCCATTTTTTAGTCAAAAGTGTTCAT
64 CTTAATCAAAAATTCCATCTTTTAGTCAAAAGTGTTCAT
* *
5549 TTTTATTTACA-AGTTAATCACAAATTCCATCTTTCA-CTTAAAAAAATCCACTCTTTATTACAA
1 TTTTATTTACAGA-TTAATCACAAATTCAATCTTTCATC-CAAAAAAATCCACTCTTTATTACAA
5612 CTTAATCAAAAATTCCATCTTTTAG
64 CTTAATCAAAAATTCCATCTTTTAG
5637 CTAAAGATTG
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
100 2 0.03
101 33 0.45
102 31 0.42
103 7 0.10
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.41
Consensus pattern (102 bp):
TTTTATTTACAGATTAATCACAAATTCAATCTTTCATCCAAAAAAATCCACTCTTTATTACAACT
TAATCAAAAATTCCATCTTTTAGTCAAAAGTGTTCAT
Found at i:5995 original size:17 final size:21
Alignment explanation
Indices: 5961--6000 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
5951 CTTTCTTCCC
5961 CTTCTTCAACGAACCC-AACT
1 CTTCTTCAACGAACCCAAACT
5981 CTTCTTCAA-G-A-CCAAACT
1 CTTCTTCAACGAACCCAAACT
5999 CT
1 CT
6001 AGTTGCAGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 2 0.11
18 7 0.37
19 1 0.05
20 9 0.47
ACGTcount: A:0.30, C:0.38, G:0.05, T:0.28
Consensus pattern (21 bp):
CTTCTTCAACGAACCCAAACT
Found at i:6000 original size:18 final size:20
Alignment explanation
Indices: 5961--6000 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
5951 CTTTCTTCCC
*
5961 CTTCTTCAACGAACCCAACT
1 CTTCTTCAACGAACCAAACT
5981 CTTCTTCAA-G-ACCAAACT
1 CTTCTTCAACGAACCAAACT
5999 CT
1 CT
6001 AGTTGCAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 1 0.05
20 9 0.47
ACGTcount: A:0.30, C:0.38, G:0.05, T:0.28
Consensus pattern (20 bp):
CTTCTTCAACGAACCAAACT
Found at i:7949 original size:84 final size:84
Alignment explanation
Indices: 7808--7980 Score: 346
Period size: 84 Copynumber: 2.1 Consensus size: 84
7798 GCAATATCTA
7808 ACTAAATACTAAATTGAGGGATAATTAATCAGCGATCTAAATTGAGCTTGGGCTGTATGATTTAA
1 ACTAAATACTAAATTGAGGGATAATTAATCAGCGATCTAAATTGAGCTTGGGCTGTATGATTTAA
7873 AATGCAACGATACTAAACT
66 AATGCAACGATACTAAACT
7892 ACTAAATACTAAATTGAGGGATAATTAATCAGCGATCTAAATTGAGCTTGGGCTGTATGATTTAA
1 ACTAAATACTAAATTGAGGGATAATTAATCAGCGATCTAAATTGAGCTTGGGCTGTATGATTTAA
7957 AATGCAACGATACTAAACT
66 AATGCAACGATACTAAACT
7976 ACTAA
1 ACTAA
7981 GTGAAATTAA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (84 bp):
ACTAAATACTAAATTGAGGGATAATTAATCAGCGATCTAAATTGAGCTTGGGCTGTATGATTTAA
AATGCAACGATACTAAACT
Found at i:16170 original size:11 final size:11
Alignment explanation
Indices: 16154--16186 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
16144 GAAGTTCGTG
16154 ATTGAAGATTT
1 ATTGAAGATTT
16165 ATTGAAGATATT
1 ATTGAAGAT-TT
16177 -TTGAAGATTT
1 ATTGAAGATTT
16187 CAAGACTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.10
11 17 0.81
12 2 0.10
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (11 bp):
ATTGAAGATTT
Found at i:20201 original size:69 final size:69
Alignment explanation
Indices: 20090--20230 Score: 255
Period size: 69 Copynumber: 2.0 Consensus size: 69
20080 TGAAACGTAC
*
20090 ATAAATCAAATAGGATTGTCAAATCTCTAATTTCATCTATAACTACCAACATACTAAATACACAA
1 ATAAATCAAATAGAATTGTCAAATCTCTAATTTCATCTATAACTACCAACATACTAAATACACAA
20155 ACAA
66 ACAA
* *
20159 ATAAATCAAATAGAATTGTCAAATCTCTAATTTCATGTATAACTACCAACCTACTAAATACACAA
1 ATAAATCAAATAGAATTGTCAAATCTCTAATTTCATCTATAACTACCAACATACTAAATACACAA
20224 ACAA
66 ACAA
20228 ATA
1 ATA
20231 GTAAATTACA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.48, C:0.20, G:0.04, T:0.28
Consensus pattern (69 bp):
ATAAATCAAATAGAATTGTCAAATCTCTAATTTCATCTATAACTACCAACATACTAAATACACAA
ACAA
Found at i:20388 original size:15 final size:16
Alignment explanation
Indices: 20368--20409 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
20358 CGAAATATAT
20368 ATATATATATAT-ACA
1 ATATATATATATCACA
*
20383 ATATATATAACATCACA
1 ATATATAT-ATATCACA
20400 ATATAT-TATA
1 ATATATATATA
20410 CTAAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 10 0.43
16 4 0.17
17 9 0.39
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATATATATATCACA
Found at i:20388 original size:17 final size:18
Alignment explanation
Indices: 20366--20410 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
20356 TTCGAAATAT
*
20366 ATATATATATATAT-ACA
1 ATATATATATACATCACA
20383 ATATATATA-ACATCACA
1 ATATATATATACATCACA
20400 ATATAT-TATAC
1 ATATATATATAC
20411 TAAATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATATATATACATCACA
Found at i:20734 original size:2 final size:2
Alignment explanation
Indices: 20727--20754 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20717 TCTTAGAATC
20727 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
20755 TAAAACTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21039 original size:21 final size:21
Alignment explanation
Indices: 21000--21049 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
20990 TTAATGAAAA
**
21000 CTTTACATAATTATGTTTATT
1 CTTTACATAATTACATTTATT
* *
21021 CTTTTCATAATTACATTTAGT
1 CTTTACATAATTACATTTATT
21042 CATTTACA
1 C-TTTACA
21050 ATGGTAGTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.52
Consensus pattern (21 bp):
CTTTACATAATTACATTTATT
Found at i:22010 original size:16 final size:16
Alignment explanation
Indices: 21991--22022 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
21981 TTTTGGTATA
21991 CATATATTCTATTTTT
1 CATATATTCTATTTTT
22007 CATATATTCTATTTTT
1 CATATATTCTATTTTT
22023 ATTTTCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (16 bp):
CATATATTCTATTTTT
Done.