Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009665.1 Corchorus capsularis cultivar CVL-1 contig09686, 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: 25727
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4660 original size:24 final size:24
Alignment explanation
Indices: 4628--4675 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
4618 ATGGAACATC
**
4628 ATGACCATCATGACCCAAACTCTT
1 ATGACCATCAAAACCCAAACTCTT
4652 ATGACCATCAAAACCCAAACTCTT
1 ATGACCATCAAAACCCAAACTCTT
4676 TGTCCCGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.33, G:0.06, T:0.23
Consensus pattern (24 bp):
ATGACCATCAAAACCCAAACTCTT
Found at i:8265 original size:25 final size:25
Alignment explanation
Indices: 8249--8296 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
8239 TTTTTTTGAT
8249 ACAAATTAAGACGTTTTGTTTATGA
1 ACAAATTAAGACGTTTTGTTTATGA
**
8274 AGTAATTAAGACGTTTTGTTTAT
1 ACAAATTAAGACGTTTTGTTTAT
8297 ATCATTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (25 bp):
ACAAATTAAGACGTTTTGTTTATGA
Found at i:12521 original size:12 final size:12
Alignment explanation
Indices: 12504--12529 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12494 CAATTATCTT
12504 TAATTATATATA
1 TAATTATATATA
12516 TAATTATATATA
1 TAATTATATATA
12528 TA
1 TA
12530 GTTTAGGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATTATATATA
Found at i:12649 original size:21 final size:21
Alignment explanation
Indices: 12624--12664 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
12614 TCATGTTGTG
12624 TCGTGTCCCGTGTACACGTTA
1 TCGTGTCCCGTGTACACGTTA
12645 TCGTGTCCCGTGTACACGTT
1 TCGTGTCCCGTGTACACGTT
12665 TATAAACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.29, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGTGTCCCGTGTACACGTTA
Found at i:12888 original size:33 final size:33
Alignment explanation
Indices: 12846--12908 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
12836 GATTGTCAGG
12846 TCTATAAATAACTTAACTACACTAAAGAATTCT
1 TCTATAAATAACTTAACTACACTAAAGAATTCT
12879 TCTATAAATAACTTAACTACACTAAAGAAT
1 TCTATAAATAACTTAACTACACTAAAGAAT
12909 AGAAATTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.32
Consensus pattern (33 bp):
TCTATAAATAACTTAACTACACTAAAGAATTCT
Found at i:15889 original size:88 final size:89
Alignment explanation
Indices: 15795--15957 Score: 274
Period size: 88 Copynumber: 1.8 Consensus size: 89
15785 GGGACAGCTT
**
15795 AAAAAATGGGGACAAATTAAAAGCCAAGGGGGCCAAATTAGAAAATAAAAATCATGGGGG-GCCA
1 AAAAAATGGGGACAAATTAAAAAACAAGGGGGCCAAATTAGAAAATAAAAATCATGGGGGAGCCA
15859 AAACAAGATTTGGGCCAGCTTAAA
66 AAACAAGATTTGGGCCAGCTTAAA
* *
15883 AAAAAATGGGGACAAATTAAAAAACAAGGGGGCGAAATTAGAAAATAAAAATCATGGGGGAGCCG
1 AAAAAATGGGGACAAATTAAAAAACAAGGGGGCCAAATTAGAAAATAAAAATCATGGGGGAGCCA
*
15948 AAACAGGATT
66 AAACAAGATT
15958 AACCATTTTA
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 57 0.83
89 12 0.17
ACGTcount: A:0.48, C:0.12, G:0.26, T:0.14
Consensus pattern (89 bp):
AAAAAATGGGGACAAATTAAAAAACAAGGGGGCCAAATTAGAAAATAAAAATCATGGGGGAGCCA
AAACAAGATTTGGGCCAGCTTAAA
Found at i:15902 original size:21 final size:21
Alignment explanation
Indices: 15878--15932 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
15868 TTGGGCCAGC
15878 TTAAAAAAAAATGGGGAC-AAA
1 TTAAAAAAAAA-GGGGACGAAA
* *
15899 TTAAAAAACAAGGGGGCGAAA
1 TTAAAAAAAAAGGGGACGAAA
15920 TTAGAAAATAAAA
1 TTA-AAAA-AAAA
15933 ATCATGGGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 5 0.18
21 16 0.57
22 4 0.14
23 3 0.11
ACGTcount: A:0.60, C:0.05, G:0.20, T:0.15
Consensus pattern (21 bp):
TTAAAAAAAAAGGGGACGAAA
Found at i:21809 original size:60 final size:60
Alignment explanation
Indices: 21731--21848 Score: 218
Period size: 60 Copynumber: 2.0 Consensus size: 60
21721 AAATAACCTC
21731 CTTAAATTTAGGCACGATTTTAGCCCAAGGTTTAACCCCCTTTTAAAATAAATTCTCTTT
1 CTTAAATTTAGGCACGATTTTAGCCCAAGGTTTAACCCCCTTTTAAAATAAATTCTCTTT
**
21791 CTTAAATTTAGGCACGATTTTAGCCCAAGGTTTAGTCCCCTTTTAAAATAAATTCTCT
1 CTTAAATTTAGGCACGATTTTAGCCCAAGGTTTAACCCCCTTTTAAAATAAATTCTCT
21849 ATAAAGGGTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (60 bp):
CTTAAATTTAGGCACGATTTTAGCCCAAGGTTTAACCCCCTTTTAAAATAAATTCTCTTT
Found at i:25545 original size:16 final size:13
Alignment explanation
Indices: 25541--25596 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 13
25531 TATATTATTA
*
25541 TTATTATATTTAT
1 TTATTTTATTTAT
25554 TTA-TTTATTTAT
1 TTATTTTATTTAT
* * *
25566 TTATATTCTATAT
1 TTATTTTATTTAT
25579 TTATTATTATTTAT
1 TTATT-TTATTTAT
25593 TTAT
1 TTAT
25597 ACTTTAATTA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
12 11 0.32
13 13 0.38
14 10 0.29
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:25556 original size:4 final size:4
Alignment explanation
Indices: 25541--25596 Score: 62
Period size: 4 Copynumber: 14.0 Consensus size: 4
25531 TATATTATTA
* *
25541 TTAT TATAT TTAT TTAT TTAT TTAT TTAT ATTCT ATAT TTA- TTA- TTAT
1 TTAT T-TAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT
25589 TTAT TTAT
1 TTAT TTAT
25597 ACTTTAATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
3 6 0.13
4 32 0.71
5 7 0.16
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:25559 original size:35 final size:38
Alignment explanation
Indices: 25520--25596 Score: 90
Period size: 39 Copynumber: 2.1 Consensus size: 38
25510 ATCTAATAAG
25520 TATT-TGTATTGTATATTAT-TA-TTATTA-TATTTATT
1 TATTATGTATT-TATATTATATATTTATTATTATTTATT
* *
25555 TATTTATTTATTTATATTCTATATTTATTATTATTTATT
1 TA-TTATGTATTTATATTATATATTTATTATTATTTATT
25594 TAT
1 TAT
25597 ACTTTAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
35 2 0.06
36 9 0.26
37 7 0.20
38 7 0.20
39 10 0.29
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.68
Consensus pattern (38 bp):
TATTATGTATTTATATTATATATTTATTATTATTTATT
Done.