Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010717.1 Corchorus capsularis cultivar CVL-1 contig10738, 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: 8702
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:1075 original size:23 final size:23
Alignment explanation
Indices: 1012--1077 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 23
1002 AGTGGTTCCG
*
1012 TACAAAATTATGTACATGTTGTCA
1 TACAAAATTATGTACATG-TATCA
*
1036 CA-AAATATTATGT--ATGTATCA
1 TACAAA-ATTATGTACATGTATCA
1057 TACAAAATTATGTACATGTAT
1 TACAAAATTATGTACATGTAT
1078 TGTATTGCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
21 12 0.34
22 6 0.17
23 9 0.26
24 8 0.23
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (23 bp):
TACAAAATTATGTACATGTATCA
Found at i:2137 original size:35 final size:35
Alignment explanation
Indices: 2098--2166 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
2088 CGATTTGGCT
2098 TTCTGATGGATCTTGGGCAGTAGTTATTGTAATTA
1 TTCTGATGGATCTTGGGCAGTAGTTATTGTAATTA
2133 TTCTGATGGATCTTGGGCAGTAGTTATTGTAATT
1 TTCTGATGGATCTTGGGCAGTAGTTATTGTAATT
2167 TAGAACTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (35 bp):
TTCTGATGGATCTTGGGCAGTAGTTATTGTAATTA
Found at i:5533 original size:21 final size:20
Alignment explanation
Indices: 5462--5551 Score: 72
Period size: 21 Copynumber: 4.3 Consensus size: 20
5452 CTGATCACCC
*
5462 TTTACTCTTTATTGATTACTAT
1 TTTACTC-TTACTGATTA-TAT
* * *
5484 TTGACTCTTACTAATTATCAC
1 TTTACTCTTACTGATTAT-AT
* *
5505 TTTGCTCTTACTGGTTACTAT
1 TTTACTCTTACTGATTA-TAT
* *
5526 TTTACTCTTACTGGTTATCT
1 TTTACTCTTACTGATTATAT
5546 TTTACT
1 TTTACT
5552 GATTACTATT
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
20 9 0.16
21 39 0.71
22 7 0.13
ACGTcount: A:0.20, C:0.19, G:0.08, T:0.53
Consensus pattern (20 bp):
TTTACTCTTACTGATTATAT
Found at i:5557 original size:21 final size:21
Alignment explanation
Indices: 5512--5558 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
5502 CACTTTGCTC
*
5512 TTACTGGTTACTATTTTACTC
1 TTACTGGTTACTATTTTACTA
*
5533 TTACTGGTTA-TCTTTTACTGA
1 TTACTGGTTACTATTTTACT-A
5554 TTACT
1 TTACT
5559 ATTTTACTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (21 bp):
TTACTGGTTACTATTTTACTA
Found at i:5572 original size:22 final size:22
Alignment explanation
Indices: 5546--5944 Score: 162
Period size: 22 Copynumber: 18.5 Consensus size: 22
5536 CTGGTTATCT
5546 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
*
5568 TTTAC-G-----GATTTTACTC
1 TTTACTGATTACTATTTTACTC
* *
5584 TTTACTGATTACCT-TCTTACTT
1 TTTACTGATTA-CTATTTTACTC
*
5606 TTTACTGATTACCATTTTACTC
1 TTTACTGATTACTATTTTACTC
* *
5628 TTTTACTGATTACCATTTTCTGCTCC
1 -TTTACTGATTACTA-TTT-TACT-C
* *
5654 TTTTTTTACTGATTACTCTTTTACTT
1 ----TTTACTGATTACTATTTTACTC
* * * *
5680 TTTACTGATT-GTCTTTTGCTT
1 TTTACTGATTACTATTTTACTC
* *
5701 TTTATTGATTACCT-TTTTA-TT
1 TTTACTGATTA-CTATTTTACTC
5722 TCTTACTGATTAGCT-TTTTACTC
1 T-TTACTGATTA-CTATTTTACTC
* *
5745 TTTACTGATCACCT-TTTCACTC
1 TTTACTGATTA-CTATTTTACTC
* *
5767 -TTACTGATTTC-CTTTTACT-
1 TTTACTGATTACTATTTTACTC
*
5786 TCTTACTTG-TTACTTTTTTACTC
1 T-TTAC-TGATTACTATTTTACTC
*
5809 -TTACTGATTACTATTTTACATT
1 TTTACTGATTACTATTTTAC-TC
* * *
5831 TTTACTGACTATTATTTCACT-
1 TTTACTGATTACTATTTTACTC
** * *
5852 TTTGTTGATTACCT-TCTTACTT
1 TTTACTGATTA-CTATTTTACTC
* *
5874 TTTAATGATTAC-CTTTTACTC
1 TTTACTGATTACTATTTTACTC
* * * *
5895 -TTACTAACTACCATTTTACCC
1 TTTACTGATTACTATTTTACTC
* *
5916 TTT-CAGA-TACT-TTTTACTT
1 TTTACTGATTACTATTTTACTC
5935 TTTACTGATT
1 TTTACTGATT
5945 GCATGCTATT
Statistics
Matches: 288, Mismatches: 54, Indels: 71
0.70 0.13 0.17
Matches are distributed among these distances:
16 14 0.05
17 1 0.00
19 9 0.03
20 23 0.08
21 83 0.29
22 99 0.34
23 33 0.11
24 3 0.01
25 3 0.01
26 1 0.00
27 3 0.01
28 3 0.01
29 13 0.05
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (22 bp):
TTTACTGATTACTATTTTACTC
Found at i:5580 original size:16 final size:16
Alignment explanation
Indices: 5559--5593 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5549 ACTGATTACT
5559 ATTTTACTCTTTACGG
1 ATTTTACTCTTTACGG
*
5575 ATTTTACTCTTTACTG
1 ATTTTACTCTTTACGG
5591 ATT
1 ATT
5594 ACCTTCTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.54
Consensus pattern (16 bp):
ATTTTACTCTTTACGG
Found at i:5609 original size:45 final size:46
Alignment explanation
Indices: 5554--5896 Score: 129
Period size: 43 Copynumber: 7.7 Consensus size: 46
5544 CTTTTACTGA
* *
5554 TTACTATTTTACTCTTTACGGATTTTACTC-TTTACTGATTACCTTC
1 TTACTATTTTACTCATTAC-CATTTTACTCTTTTACTGATTACCTTC
*
5600 TTACT-TTTTACTGATTACCATTTTACTCTTTTACTGATTACCATTTTC
1 TTACTATTTTACTCATTACCATTTTACTCTTTTACTGATTACC---TTC
* * * **
5648 TGCTCCTTTTTTTACTGATTACTC-TTTTACT-TTTTACTGATTGTCTT-
1 T--TAC-TATTTTACTCATTAC-CATTTTACTCTTTTACTGATTACCTTC
* * * * * *
5695 TTGCT-TTTTATTGATTACCTTTTTA-T-TTCTTACTGATTAGCTTT
1 TTACTATTTTACTCATTACCATTTTACTCTT-TTACTGATTACCTTC
* * * *
5739 TTACT-CTTTACTGATCACC-TTTTCACTC--TTACTGATTTCCTT-
1 TTACTATTTTACTCATTACCATTTT-ACTCTTTTACTGATTACCTTC
* ** ** *
5781 TTACT-TCTTACTTGTTACTTTTTTACTC--TTACTGATTA-CTATT
1 TTACTATTTTACTCATTACCATTTTACTCTTTTACTGATTACCT-TC
* * ** *
5824 TTAC-ATTTTTACTGACTATTATTTCACT-TTTGT--TGATTACCTTC
1 TTACTA-TTTTACTCATTACCATTTTACTCTTT-TACTGATTACCTTC
* *
5868 TTACT-TTTTAATGATTACC-TTTTACTCTT
1 TTACTATTTTACTCATTACCATTTTACTCTT
5897 ACTAACTACC
Statistics
Matches: 235, Mismatches: 36, Indels: 55
0.72 0.11 0.17
Matches are distributed among these distances:
41 2 0.01
42 37 0.16
43 65 0.28
44 52 0.22
45 30 0.13
46 6 0.03
47 1 0.00
48 6 0.03
50 2 0.01
51 13 0.06
52 20 0.09
53 1 0.00
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.56
Consensus pattern (46 bp):
TTACTATTTTACTCATTACCATTTTACTCTTTTACTGATTACCTTC
Found at i:5694 original size:21 final size:21
Alignment explanation
Indices: 5656--5893 Score: 141
Period size: 21 Copynumber: 11.0 Consensus size: 21
5646 TCTGCTCCTT
5656 TTTTTACTGATTACTCTTTTAC
1 TTTTTACTGATTA-TCTTTTAC
* *
5678 TTTTTACTGATTGTCTTTTGC
1 TTTTTACTGATTATCTTTTAC
* *
5699 TTTTTATTGATTACCTTTTTA-
1 TTTTTACTGATTATC-TTTTAC
*
5720 TTTCTTACTGATTAGCTTTTTAC
1 TTT-TTACTGATTATC-TTTTAC
* * *
5743 TCTTTACTGATCACCTTTTCAC
1 TTTTTACTGATTATCTTTT-AC
*
5765 -TCTTACTGATT-TCCTTTTAC
1 TTTTTACTGATTAT-CTTTTAC
* *
5785 TTCTTACTTG-TTACTTTTTTAC
1 TTTTTAC-TGATTA-TCTTTTAC
* *
5807 -TCTTACTGATTACTATTTTAC
1 TTTTTACTGATTA-TCTTTTAC
*
5828 ATTTTTACTGACTAT-TATTTCAC
1 -TTTTTACTGATTATCT-TTT-AC
*
5851 TTTTGT--TGATTACCTTCTTAC
1 TTTT-TACTGATTATCTT-TTAC
* *
5872 TTTTTAATGATTACCTTTTAC
1 TTTTTACTGATTATCTTTTAC
5893 T
1 T
5894 CTTACTAACT
Statistics
Matches: 176, Mismatches: 21, Indels: 39
0.75 0.09 0.17
Matches are distributed among these distances:
20 5 0.03
21 82 0.47
22 73 0.41
23 16 0.09
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.57
Consensus pattern (21 bp):
TTTTTACTGATTATCTTTTAC
Found at i:5719 original size:43 final size:42
Alignment explanation
Indices: 5656--5899 Score: 169
Period size: 43 Copynumber: 5.7 Consensus size: 42
5646 TCTGCTCCTT
* *
5656 TTTTTACTGATTA-CTCTTTTACTTTTTACTGATTGTCTTTTGC
1 TTTTTACTGATTACCT-TTTTAC-TCTTACTGATTGTCTTTTAC
* *
5699 TTTTTATTGATTACCTTTTTATTTCTTACTGATTAG-CTTTTTAC
1 TTTTTACTGATTACCTTTTTA-CTCTTACTGATT-GTC-TTTTAC
* * *
5743 TCTTTACTGATCACCTTTTCACTCTTACTGATT-TCCTTTTAC
1 TTTTTACTGATTACCTTTTTACTCTTACTGATTGT-CTTTTAC
* * * *
5785 TTCTTACTTG-TTACTTTTTTACTCTTACTGATTACTATTTTAC
1 TTTTTAC-TGATTACCTTTTTACTCTTACTGATT-GTCTTTTAC
* * ** **
5828 ATTTTTACTGACTA--TTATTTCACTTTTGTTGATTACCTTCTTAC
1 -TTTTTACTGATTACCTT-TTT-ACTCTTACTGATTGTCTT-TTAC
*
5872 TTTTTAATGATTACC-TTTTACTCTTACT
1 TTTTTACTGATTACCTTTTTACTCTTACT
5900 AACTACCATT
Statistics
Matches: 157, Mismatches: 28, Indels: 33
0.72 0.13 0.15
Matches are distributed among these distances:
42 39 0.25
43 69 0.44
44 49 0.31
ACGTcount: A:0.18, C:0.19, G:0.06, T:0.57
Consensus pattern (42 bp):
TTTTTACTGATTACCTTTTTACTCTTACTGATTGTCTTTTAC
Found at i:5849 original size:86 final size:84
Alignment explanation
Indices: 5658--5918 Score: 219
Period size: 86 Copynumber: 3.0 Consensus size: 84
5648 TGCTCCTTTT
* * *
5658 TTTACTGATTACTCTTTT-ACTTTTTACTGATTGT-CTTTTGCTTTTTATTGATTACCTTTTTAT
1 TTTACTGATCAC-CTTTTCAC-TCTTACTGATT-TCCTTTTACTTTTTATTGATTA-CTTTTTA-
*
5721 TTCTTACTGATTAGCT-TTTTACTC
61 CTCTTACTGATTA-CTATTTTACTC
*
5745 TTTACTGATCACCTTTTCACTCTTACTGATTTCCTTTTACTTCTTACTTG-TTACTTTTTTACTC
1 TTTACTGATCACCTTTTCACTCTTACTGATTTCCTTTTACTTTTTA-TTGATTAC-TTTTTACTC
*
5809 TTACTGATTACTATTTTACATT
64 TTACTGATTACTATTTTAC-TC
* * ** * * *
5831 TTTACTGA-CTA-TTATTTCACTTTTGTTGATTACCTTCTTACTTTTTAATGATTACCTTTTACT
1 TTTACTGATC-ACCT-TTTCACTCTTACTGATTTCCTT-TTACTTTTTATTGATTACTTTTTACT
* * * *
5894 CTTACTAACTACCATTTTACCC
63 CTTACTGATTACTATTTTACTC
5916 TTT
1 TTT
5919 CAGATACTTT
Statistics
Matches: 145, Mismatches: 19, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
84 2 0.01
85 25 0.17
86 89 0.61
87 29 0.20
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.56
Consensus pattern (84 bp):
TTTACTGATCACCTTTTCACTCTTACTGATTTCCTTTTACTTTTTATTGATTACTTTTTACTCTT
ACTGATTACTATTTTACTC
Found at i:6301 original size:55 final size:55
Alignment explanation
Indices: 6221--6365 Score: 184
Period size: 55 Copynumber: 2.6 Consensus size: 55
6211 GATTACTATC
* * * * *
6221 TTTTACCTGATTACTAATTTGCTGATTACTATTACCTTAACTCTGATTAATCTCT
1 TTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAACCTCT
** * * *
6276 TTTTACTTAATTACTGATTTACTGATTACTGCTACTTTGACTCTGATTTACCTCT
1 TTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAACCTCT
6331 TTTTACTTAATTACTGATTTACTGACTT-CTATTAC
1 TTTTACTTAATTACTGATTTACTGA-TTACTATTAC
6366 TCTTTACTGA
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
55 75 0.97
56 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.08, T:0.49
Consensus pattern (55 bp):
TTTTACTTAATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAACCTCT
Found at i:6390 original size:22 final size:22
Alignment explanation
Indices: 6362--6421 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
6352 CTGACTTCTA
*
6362 TTACTCTTTACTGATTATCACT
1 TTACTCTTTACTGATTACCACT
*
6384 TTACTCTTTACTGATTACCATT
1 TTACTCTTTACTGATTACCACT
6406 TTAC-CTTTTACTGATT
1 TTACTC-TTTACTGATT
6422 GCATCTTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.52
Consensus pattern (22 bp):
TTACTCTTTACTGATTACCACT
Done.