Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006519.1 Corchorus capsularis cultivar CVL-1 contig06540, 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: 22343
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:4747 original size:26 final size:26
Alignment explanation
Indices: 4707--4766 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
4697 TTTTATTTCT
*
4707 TGATTACCATTTTTTA-CTCTTTGTAC
1 TGATTACCATATTTTACCT-TTTGTAC
* *
4733 TGATTACTATATTTTACCTTTTTTAC
1 TGATTACCATATTTTACCTTTTGTAC
4759 TGATTACC
1 TGATTACC
4767 TCTTTTTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 27 0.93
27 2 0.07
ACGTcount: A:0.22, C:0.18, G:0.07, T:0.53
Consensus pattern (26 bp):
TGATTACCATATTTTACCTTTTGTAC
Found at i:4773 original size:26 final size:25
Alignment explanation
Indices: 4707--4834 Score: 73
Period size: 26 Copynumber: 4.8 Consensus size: 25
4697 TTTTATTTCT
4707 TGATTACCATTTTTTACTCTTTGTAC
1 TGATTACC-TTTTTTACTCTTTGTAC
*
4733 TGATTA-CTATATTTTAC-CTTTTTTAC
1 TGATTACCT-T-TTTTACTC-TTTGTAC
*
4759 TGATTACCTCTTTTT-CTTTCTGCTTCTAC
1 TGATTACCT-TTTTTAC--TCT--TTGTAC
* * *
4788 TGAATACCGCTTTTTACTCTTTTTAC
1 TGATTACC-TTTTTTACTCTTTGTAC
*
4814 TTAATTACCATTTTTTACTCT
1 -TGATTACC-TTTTTTACTCT
4835 CCTTTTTTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
24 1 0.01
25 4 0.05
26 33 0.41
27 20 0.25
28 4 0.05
29 17 0.21
30 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.05, T:0.55
Consensus pattern (25 bp):
TGATTACCTTTTTTACTCTTTGTAC
Found at i:4877 original size:18 final size:19
Alignment explanation
Indices: 4856--4895 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
4846 TTTTACTTAA
* *
4856 TACCATTTTTA-CTCTTTT
1 TACCACTTTTATCCCTTTT
4874 TACCACTTTTATCCCTTTT
1 TACCACTTTTATCCCTTTT
4893 TAC
1 TAC
4896 TGAATACCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.55
Consensus pattern (19 bp):
TACCACTTTTATCCCTTTT
Found at i:4909 original size:26 final size:26
Alignment explanation
Indices: 4874--4949 Score: 77
Period size: 26 Copynumber: 2.9 Consensus size: 26
4864 TTACTCTTTT
4874 TACCAC-TTTTATCCCTTTTTACTGAA
1 TACCACTTTTTA-CCCTTTTTACTGAA
*
4900 TACCACTTTTTACTCTTTTTACTG-A
1 TACCACTTTTTACCCTTTTTACTGAA
*
4925 TCACCA-TTTCTTACTCTTTATTACT
1 T-ACCACTTT-TTACCCTTT-TTACT
4950 AATTACTCTC
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
25 5 0.11
26 30 0.67
27 10 0.22
ACGTcount: A:0.21, C:0.26, G:0.03, T:0.50
Consensus pattern (26 bp):
TACCACTTTTTACCCTTTTTACTGAA
Found at i:5465 original size:55 final size:55
Alignment explanation
Indices: 5400--5549 Score: 246
Period size: 55 Copynumber: 2.7 Consensus size: 55
5390 CACTTTACTG
*
5400 ATTAATCTCTTTTTACTTAATTATTGATTTACTAATTACTATTACCTTGATTCTA
1 ATTAATCTCTTTTTACTTAATTACTGATTTACTAATTACTATTACCTTGATTCTA
* *
5455 ATTAATCTCTTTTTACTTAATTACTGGTTTACTGATTACTATTACCTTGATTCTA
1 ATTAATCTCTTTTTACTTAATTACTGATTTACTAATTACTATTACCTTGATTCTA
* * *
5510 ATTAATCTCTTTTTACTTAATTACCGGTTTACTGATTACT
1 ATTAATCTCTTTTTACTTAATTACTGATTTACTAATTACT
5550 CTTTTACTTT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 91 1.00
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.51
Consensus pattern (55 bp):
ATTAATCTCTTTTTACTTAATTACTGATTTACTAATTACTATTACCTTGATTCTA
Found at i:5565 original size:22 final size:21
Alignment explanation
Indices: 5537--5751 Score: 179
Period size: 22 Copynumber: 10.0 Consensus size: 21
5527 TAATTACCGG
5537 TTTACTGATTACTCTTTTACTT
1 TTTACTGATTAC-CTTTTACTT
* *
5559 TTTACTGATTGCCTTTTTGCTT
1 TTTACTGATTACC-TTTTACTT
5581 TTTACTGATTACCTTTTACTT
1 TTTACTGATTACCTTTTACTT
* * *
5602 CTTACTGATTAGCTTTTTACTC
1 TTTACTGATTA-CCTTTTACTT
5624 TTTACTGATTACCATTTTAC-T
1 TTTACTGATTACC-TTTTACTT
* *
5645 CTTGCTGATTACCTTCTTACTT
1 TTTACTGATTACCTT-TTACTT
*
5667 TTTACT-AGTTA-CTACTTTACTC
1 TTTACTGA-TTACCT--TTTACTT
* *
5689 TTTACTAATTACCATTTTACCT
1 TTTACTGATTACC-TTTTACTT
* *
5711 TTTACTGATTATC-ATT-CTTT
1 TTTACTGATTACCTTTTAC-TT
*
5731 TTTACTGATTACTATTTTACT
1 TTTACTGATTAC-CTTTTACT
5752 ATTTGAATTT
Statistics
Matches: 154, Mismatches: 24, Indels: 30
0.74 0.12 0.14
Matches are distributed among these distances:
19 1 0.01
20 16 0.10
21 37 0.24
22 95 0.62
23 4 0.03
24 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.54
Consensus pattern (21 bp):
TTTACTGATTACCTTTTACTT
Found at i:5607 original size:43 final size:43
Alignment explanation
Indices: 5537--5721 Score: 182
Period size: 43 Copynumber: 4.3 Consensus size: 43
5527 TAATTACCGG
* *
5537 TTTACTGATTACTCTTTTACTTTTTACTGATTGCCTTTTTGCTT
1 TTTACTGATTAC-CTTTTACTTCTTACTGATTGCCTTTTTACTT
*
5581 TTTACTGATTACCTTTTACTTCTTACTGATTAG-CTTTTTACTC
1 TTTACTGATTACCTTTTACTTCTTACTGATT-GCCTTTTTACTT
* * *
5624 TTTACTGATTACCATTTTAC-TCTTGCTGATTACCTTCTTACTT
1 TTTACTGATTACC-TTTTACTTCTTACTGATTGCCTTTTTACTT
* * * *
5667 TTTACT-AGTTA-CTACTTTAC-TCTTTACTAATTACCATTTTACCT
1 TTTACTGA-TTACCT--TTTACTTC-TTACTGATTGCCTTTTTACTT
5711 TTTACTGATTA
1 TTTACTGATTA
5722 TCATTCTTTT
Statistics
Matches: 121, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
41 1 0.01
42 2 0.02
43 73 0.60
44 44 0.36
45 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.54
Consensus pattern (43 bp):
TTTACTGATTACCTTTTACTTCTTACTGATTGCCTTTTTACTT
Found at i:5620 original size:65 final size:65
Alignment explanation
Indices: 5538--5751 Score: 242
Period size: 65 Copynumber: 3.3 Consensus size: 65
5528 AATTACCGGT
* * * * *
5538 TTACTGATTACTCTTTTACTTTTTACTGATTGCCTTTTTGCTTTTTACTGATTACCTT-TTACTT
1 TTACTGATTACTATTTTACTCTTTACTGATTACCATTTTAC-TTTTACTGATTACCTTCTTACTT
5602 C
65 C
* *
5603 TTACTGATTAGCT-TTTTACTCTTTACTGATTACCATTTTACTCTTGCTGATTACCTTCTTACTT
1 TTACTGATTA-CTATTTTACTCTTTACTGATTACCATTTTACTTTTACTGATTACCTTCTTACTT
*
5667 T
65 C
* * *
5668 TTACT-AGTTACTACTTTACTCTTTACTAATTACCATTTTACCTTTTACTGATTATCATTCTT--
1 TTACTGA-TTACTATTTTACTCTTTACTGATTACCATTTTA-CTTTTACTGATTA-CCTTCTTAC
5730 TT-
63 TTC
5732 TTACTGATTACTATTTTACT
1 TTACTGATTACTATTTTACT
5752 ATTTGAATTT
Statistics
Matches: 129, Mismatches: 13, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
64 34 0.26
65 76 0.59
66 13 0.10
67 6 0.05
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.54
Consensus pattern (65 bp):
TTACTGATTACTATTTTACTCTTTACTGATTACCATTTTACTTTTACTGATTACCTTCTTACTTC
Found at i:5845 original size:31 final size:30
Alignment explanation
Indices: 5790--5857 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
5780 TTTACTTTTT
*
5790 ACTGATTGCTTTTTCTCATTGAACTTAATC
1 ACTGATTACTTTTTCTCATTGAACTTAATC
* * *
5820 ACTGATTATTTTTTCCTTATTGAACTTAATT
1 ACTGATTACTTTTT-CTCATTGAACTTAATC
5851 ACTGATT
1 ACTGATT
5858 GCCCTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 12 0.36
31 21 0.64
ACGTcount: A:0.25, C:0.16, G:0.09, T:0.50
Consensus pattern (30 bp):
ACTGATTACTTTTTCTCATTGAACTTAATC
Found at i:9672 original size:27 final size:28
Alignment explanation
Indices: 9605--9683 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 28
9595 AAATAATCCT
* *
9605 TAAACGCAAAGAATGACCAAAATGCCCCC
1 TAAATGCAAA-AATGACCAAAATGACCCC
* *
9634 TGAGTGTC-AAAATGACCAAAAT-ACCCC
1 TAAATG-CAAAAATGACCAAAATGACCCC
*
9661 TAAATGCAAAAAAGACCAAAATG
1 TAAATGCAAAAATGACCAAAATG
9684 CTAACTCGAC
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 12 0.30
29 5 0.12
30 1 0.03
ACGTcount: A:0.48, C:0.24, G:0.14, T:0.14
Consensus pattern (28 bp):
TAAATGCAAAAATGACCAAAATGACCCC
Found at i:10330 original size:21 final size:21
Alignment explanation
Indices: 10271--10330 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
10261 CACTATTTAG
*
10271 GTACTGTACAAATGAGATT-A
1 GTACTGTACAGATGAGATTAA
* * *
10291 -CACTGTACAGATCAAATTAA
1 GTACTGTACAGATGAGATTAA
10311 GTACTGTACAGATGAGATTA
1 GTACTGTACAGATGAGATTA
10331 TTGTAGTGAC
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
19 14 0.45
20 1 0.03
21 16 0.52
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Consensus pattern (21 bp):
GTACTGTACAGATGAGATTAA
Found at i:21524 original size:28 final size:28
Alignment explanation
Indices: 21476--21529 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
21466 AACTTGTATG
21476 ATTTTGACGTTTTATCTCCTAAACTTTA
1 ATTTTGACGTTTTATCTCCTAAACTTTA
*
21504 ATTTTGGACGTTTTGTC-CCTAAACTT
1 ATTTT-GACGTTTTATCTCCTAAACTT
21530 GCAATTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (28 bp):
ATTTTGACGTTTTATCTCCTAAACTTTA
Found at i:21535 original size:29 final size:28
Alignment explanation
Indices: 21476--21536 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
21466 AACTTGTATG
*
21476 ATTTTGACGTTTTATCTCCTAAACTTTA
1 ATTTTGACGTTTTATCTCCTAAACTTCA
*
21504 ATTTTGGACGTTTTGTC-CCTAAACTTGCA
1 ATTTT-GACGTTTTATCTCCTAAACTT-CA
21533 ATTT
1 ATTT
21537 AAAACCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.48
Consensus pattern (28 bp):
ATTTTGACGTTTTATCTCCTAAACTTCA
Found at i:22305 original size:2 final size:2
Alignment explanation
Indices: 22300--22341 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
22290 ATCATAGTTA
22300 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
22342 CA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.