Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009594.1 Corchorus capsularis cultivar CVL-1 contig09615, 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: 27949
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:15025 original size:1 final size:1
Alignment explanation
Indices: 15019--15049 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
15009 CCACAACTGG
15019 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15050 CCTAAGTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21292 original size:21 final size:21
Alignment explanation
Indices: 21268--21308 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
21258 AACAAGCAAA
21268 ATTTCAAGGCCAAAGGCAAGG
1 ATTTCAAGGCCAAAGGCAAGG
*
21289 ATTTTAAGGCCAAAGGCAAG
1 ATTTCAAGGCCAAAGGCAAG
21309 AAAGACAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.17, G:0.27, T:0.17
Consensus pattern (21 bp):
ATTTCAAGGCCAAAGGCAAGG
Found at i:24822 original size:50 final size:50
Alignment explanation
Indices: 24755--25076 Score: 406
Period size: 50 Copynumber: 6.5 Consensus size: 50
24745 TTTGTTTATT
*
24755 CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTCCTTTATTTGTTTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTATTTCCTTTATTTGTTTC
*
24805 CCAAAATGCCCCTTCCCGGTTGGAAGGTCACTATTTCCTTTATTTGTTTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTATTTCCTTTATTTGTTTC
* * *
24855 CCAAAATGCCCCTTCCCGGTCGGAAGGTCACAATTTTCTTT-TCTT-ATTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTATTTCCTTTAT-TTGTTTC
* * * * *
24904 CAAAAATGCCCCTTCCCGGTCGGAAGGTCAC-ACTTCTCTTT-GTT-TATA
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTATTTC-CTTTATTTGTTTC
* * *
24952 CCAAAAAGCCCCTTCCCGATCGGAAGGTCACTGTTTCCTTTATTTGTTTC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTATTTCCTTTATTTGTTTC
* * * * *
25002 CCAAAATGCCCCTTCCTGGTTGGAAGGTC-C-AGTTTTCTTTCTTTGTTCC
1 CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTA-TTTCCTTTATTTGTTTC
25051 CCAAAATGCCCCTTCCCGGTCGGAAG
1 CCAAAATGCCCCTTCCCGGTCGGAAG
25077 TTCCCAGTTT
Statistics
Matches: 235, Mismatches: 31, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
48 38 0.16
49 82 0.35
50 115 0.49
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.34
Consensus pattern (50 bp):
CCAAAATGCCCCTTCCCGGTCGGAAGGTCACTATTTCCTTTATTTGTTTC
Found at i:25027 original size:147 final size:147
Alignment explanation
Indices: 24743--25076 Score: 460
Period size: 147 Copynumber: 2.3 Consensus size: 147
24733 CACCTATATC
* ** * * *
24743 TCTTTGTTTATTCCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTCCTTTATTTGTTTCCCA
1 TCTTTCTTTATTCCAAAATGCCCCTTCCCGGTCGGAAGGTCACACTTTCCTTTAGTTGTATACCA
* * *
24808 AAATGCCCCTTCCCGGTTGGAAGGTCACTATTTCCTTTATTTGTTTCCCAAAATGCCCCTTCCCG
66 AAAAGCCCCTTCCCGATCGGAAGGTCACTATTTCCTTTATTTGTTTCCCAAAATGCCCCTTCCCG
24873 GTCGGAAGGTCACAATTT
131 GTCGGAAGGTC-CAATTT
24891 TCTTT-TCTTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAC-TTCTCTTT-GTT-TATA
1 TCTTTCT-TTATTCC-AAAATGCCCCTTCCCGGTCGGAAGGTCACACTTTC-CTTTAGTTGTATA
*
24952 CCAAAAAGCCCCTTCCCGATCGGAAGGTCACTGTTTCCTTTATTTGTTTCCCAAAATGCCCCTTC
63 CCAAAAAGCCCCTTCCCGATCGGAAGGTCACTATTTCCTTTATTTGTTTCCCAAAATGCCCCTTC
* * *
25017 CTGGTTGGAAGGTCCAGTTT
128 CCGGTCGGAAGGTCCAATTT
*
25037 TCTTTCTTTGTTCCCCAAAATGCCCCTTCCCGGTCGGAAG
1 TCTTTCTTTATT--CCAAAATGCCCCTTCCCGGTCGGAAG
25077 TTCCCAGTTT
Statistics
Matches: 167, Mismatches: 13, Indels: 13
0.87 0.07 0.07
Matches are distributed among these distances:
146 14 0.08
147 101 0.60
148 19 0.11
149 33 0.20
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (147 bp):
TCTTTCTTTATTCCAAAATGCCCCTTCCCGGTCGGAAGGTCACACTTTCCTTTAGTTGTATACCA
AAAAGCCCCTTCCCGATCGGAAGGTCACTATTTCCTTTATTTGTTTCCCAAAATGCCCCTTCCCG
GTCGGAAGGTCCAATTT
Found at i:26558 original size:10 final size:10
Alignment explanation
Indices: 26545--26570 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
26535 CATTTCTAAC
26545 AACTTCTTCA
1 AACTTCTTCA
26555 AACTTCTTCA
1 AACTTCTTCA
26565 AACTTC
1 AACTTC
26571 ATTTCTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (10 bp):
AACTTCTTCA
Found at i:26636 original size:26 final size:26
Alignment explanation
Indices: 26607--26724 Score: 120
Period size: 26 Copynumber: 4.7 Consensus size: 26
26597 TCCCTTCATT
26607 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
26633 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
26659 TTAAACATAAACTAA-T-AA-ACTAA
1 TTAATCATAAACTAATTAAATACTAA
* * * * * *
26682 GTAAT-TTTAACTAACTAATTA-AAA
1 TTAATCATAAACTAATTAAATACTAA
*
26706 CTAATCATAAACTAATTAA
1 TTAATCATAAACTAATTAA
26725 TATTTAAAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 9
0.77 0.13 0.09
Matches are distributed among these distances:
22 7 0.09
23 9 0.12
24 8 0.11
25 12 0.16
26 39 0.52
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:26637 original size:15 final size:15
Alignment explanation
Indices: 26607--26674 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 15
26597 TCCCTTCATT
26607 TTAATCATAAACTAA
1 TTAATCATAAACTAA
26622 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
26633 TTAATCATAAACTAA
1 TTAATCATAAACTAA
*
26648 TT-A-GAT--ACTAA
1 TTAATCATAAACTAA
*
26659 TTAAACATAAACTAA
1 TTAATCATAAACTAA
26674 T
1 T
26675 AAACTAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 16 0.37
12 1 0.02
13 8 0.19
14 1 0.02
15 17 0.40
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:26707 original size:14 final size:13
Alignment explanation
Indices: 26616--26709 Score: 63
Period size: 14 Copynumber: 7.2 Consensus size: 13
26606 TTTAATCATA
26616 AACTAATTAAA-T
1 AACTAATTAAACT
*
26628 -ACTAATTAATCAT
1 AACTAATTAAAC-T
*
26641 AAACTAATTAGA-T
1 -AACTAATTAAACT
26654 -ACTAATTAAACAT
1 AACTAATTAAAC-T
26667 AAACTAA-TAAACT
1 -AACTAATTAAACT
* *
26680 AAGTAATTTTAACT
1 AACTAA-TTAAACT
26694 AACTAATTAAAACT
1 AACTAATT-AAACT
26708 AA
1 AA
26710 TCATAAACTA
Statistics
Matches: 63, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
11 18 0.29
12 5 0.08
13 6 0.10
14 21 0.33
15 13 0.21
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (13 bp):
AACTAATTAAACT
Found at i:26747 original size:12 final size:12
Alignment explanation
Indices: 26730--26755 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
26720 ATTAATATTT
26730 AAAAAATTTAAA
1 AAAAAATTTAAA
26742 AAAAAATTTAAA
1 AAAAAATTTAAA
26754 AA
1 AA
26756 TTTTTTTTTA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAAATTTAAA
Found at i:27158 original size:17 final size:18
Alignment explanation
Indices: 27135--27177 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
27125 AACCCAAAAG
27135 AAACATGGCT-ACTAATT
1 AAACATGGCTAACTAATT
*
27152 GAACATGGCTAACTAATT
1 AAACATGGCTAACTAATT
27170 AAACATGG
1 AAACATGG
27178 TTATTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (18 bp):
AAACATGGCTAACTAATT
Done.