Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016447.1 Corchorus capsularis cultivar CVL-1 contig16468, 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: 16891
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:3771 original size:12 final size:12
Alignment explanation
Indices: 3751--3780 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3741 AGTTATTTCC
*
3751 AAAACTAGCCTT
1 AAAAGTAGCCTT
3763 AAAAGTAGCCTT
1 AAAAGTAGCCTT
3775 AAAAGT
1 AAAAGT
3781 GATAGGGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (12 bp):
AAAAGTAGCCTT
Found at i:5040 original size:3 final size:3
Alignment explanation
Indices: 5032--5058 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5022 TAGAAAGCAT
5032 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
5059 AGAACCTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5646 original size:21 final size:21
Alignment explanation
Indices: 5621--5663 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5611 CTTCCTTCCC
5621 TATCGTCAATTTTCTTTTCTT
1 TATCGTCAATTTTCTTTTCTT
5642 TATCGTCAATTTTCTTTTCTT
1 TATCGTCAATTTTCTTTTCTT
5663 T
1 T
5664 CTACACATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.19, G:0.05, T:0.63
Consensus pattern (21 bp):
TATCGTCAATTTTCTTTTCTT
Found at i:6161 original size:1 final size:1
Alignment explanation
Indices: 6150--6181 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
6140 CAGAATGAGC
*
6150 AAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6182 GGATCGTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:6892 original size:19 final size:18
Alignment explanation
Indices: 6864--6905 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
6854 AATTAATTGT
6864 TTTAATATTAAATTTTTA
1 TTTAATATTAAATTTTTA
6882 TTTATATATTAAATTTTTA
1 TTTA-ATATTAAATTTTTA
*
6901 CTTAA
1 TTTAA
6906 AAATTACTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAATATTAAATTTTTA
Found at i:6911 original size:19 final size:19
Alignment explanation
Indices: 6870--6911 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
6860 TTGTTTTAAT
* * *
6870 ATTAAATTTTTATTTATAT
1 ATTAAATTTTTACTTAAAA
6889 ATTAAATTTTTACTTAAAA
1 ATTAAATTTTTACTTAAAA
6908 ATTA
1 ATTA
6912 CTCATAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTAAATTTTTACTTAAAA
Found at i:10804 original size:33 final size:34
Alignment explanation
Indices: 10761--10824 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
10751 AAACAAATAT
* *
10761 AGAGTTTAC-AAAGAGGTTTATTAATAAAAACAA
1 AGAGTCTACAAAAGAGGTTTACTAATAAAAACAA
10794 AGAGTCTACAAAAGAGGTTTACTAATAAAAA
1 AGAGTCTACAAAAGAGGTTTACTAATAAAAA
10825 TAATTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 8 0.29
34 20 0.71
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.25
Consensus pattern (34 bp):
AGAGTCTACAAAAGAGGTTTACTAATAAAAACAA
Found at i:15495 original size:13 final size:13
Alignment explanation
Indices: 15450--15496 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
15440 ATCATTTTTA
15450 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
15463 CT-TTTTACTAATT
1 CTCTTTT-CTTACT
15476 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
15490 CTCTTTT
1 CTCTTTT
15497 TTTGATTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:15511 original size:29 final size:28
Alignment explanation
Indices: 15447--15526 Score: 76
Period size: 27 Copynumber: 2.9 Consensus size: 28
15437 TTTATCATTT
* **
15447 TTACTCTTTTCTTACTCT-TTTTACTAA
1 TTACACTTTTCTTACTCTCTTTTTTTAA
* *
15474 TTACTCTTTTCTTACTCTCTTTTTTTGA
1 TTACACTTTTCTTACTCTCTTTTTTTAA
15502 TTACCAC-TTT-TTACTCTTCTTTTTT
1 TTA-CACTTTTCTTACTC-TCTTTTTT
15527 CTTATACTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 24 0.52
28 20 0.43
29 2 0.04
ACGTcount: A:0.14, C:0.23, G:0.01, T:0.62
Consensus pattern (28 bp):
TTACACTTTTCTTACTCTCTTTTTTTAA
Found at i:15602 original size:21 final size:21
Alignment explanation
Indices: 15569--15723 Score: 102
Period size: 21 Copynumber: 7.9 Consensus size: 21
15559 ACTAATCGCC
15569 TTTTACTCTTTACTGATTACTA
1 TTTTACTC-TTACTGATTACTA
* *
15591 TTTTACTCTTACTAATTACCA
1 TTTTACTCTTACTGATTACTA
* * *
15612 TTTTGCTCTTACTGATCACTG
1 TTTTACTCTTACTGATTACTA
* *
15633 GTTTATTCTTACTGATTAC--
1 TTTTACTCTTACTGATTACTA
*
15652 -CTT--T-TTACTGATTACTA
1 TTTTACTCTTACTGATTACTA
*
15669 TTTTACTTTTTACTGATTAC--
1 TTTTAC-TCTTACTGATTACTA
*
15689 -----CTTTTACTGATTACTA
1 TTTTACTCTTACTGATTACTA
15705 TTTTACTCTTTACTGATTA
1 TTTTACTC-TTACTGATTA
15724 TCATTACCTT
Statistics
Matches: 104, Mismatches: 14, Indels: 30
0.70 0.09 0.20
Matches are distributed among these distances:
14 13 0.12
15 12 0.12
16 1 0.01
18 4 0.04
21 45 0.43
22 29 0.28
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (21 bp):
TTTTACTCTTACTGATTACTA
Found at i:15661 original size:15 final size:15
Alignment explanation
Indices: 15641--15711 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 15
15631 TGGTTTATTC
15641 TTACTGATTACCTTT
1 TTACTGATTACCTTT
15656 TTACTGATTACTATTTTACTTT
1 TTACTGATTAC-------CTTT
15678 TTACTGATTACC-TT
1 TTACTGATTACCTTT
15692 TTACTGATTA-CTATT
1 TTACTGATTACCT-TT
15707 TTACT
1 TTACT
15712 CTTTACTGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 18
0.72 0.00 0.28
Matches are distributed among these distances:
13 1 0.02
14 12 0.26
15 19 0.40
22 15 0.32
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.55
Consensus pattern (15 bp):
TTACTGATTACCTTT
Found at i:15693 original size:14 final size:14
Alignment explanation
Indices: 15671--15702 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
15661 GATTACTATT
*
15671 TTACTTTTTACTGA
1 TTACCTTTTACTGA
15685 TTACCTTTTACTGA
1 TTACCTTTTACTGA
15699 TTAC
1 TTAC
15703 TATTTTACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (14 bp):
TTACCTTTTACTGA
Found at i:15694 original size:36 final size:37
Alignment explanation
Indices: 15577--15723 Score: 165
Period size: 36 Copynumber: 3.9 Consensus size: 37
15567 CCTTTTACTC
*
15577 TTTACTGATTACTATTTTACTC-TTACTAATTACCATTTT
1 TTTACTGATTACTATTTTACTCTTTACTGATTACC---TT
* ** *
15616 GCTCTTACTGATCACTGGTTTATTC-TTACTGATTACCTT
1 --T-TTACTGATTACTATTTTACTCTTTACTGATTACCTT
*
15655 TTTACTGATTACTATTTTACTTTTTACTGATTACC-T
1 TTTACTGATTACTATTTTACTCTTTACTGATTACCTT
15691 TTTACTGATTACTATTTTACTCTTTACTGATTA
1 TTTACTGATTACTATTTTACTCTTTACTGATTA
15724 TCATTACCTT
Statistics
Matches: 93, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
36 49 0.53
37 13 0.14
39 2 0.02
41 1 0.01
42 28 0.30
ACGTcount: A:0.22, C:0.18, G:0.07, T:0.52
Consensus pattern (37 bp):
TTTACTGATTACTATTTTACTCTTTACTGATTACCTT
Found at i:15772 original size:22 final size:22
Alignment explanation
Indices: 15746--15787 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
15736 ACCCCCTTTT
*
15746 TTTTACTGATTACCTTTTACTA
1 TTTTACTCATTACCTTTTACTA
*
15768 TTTTACTCTTTACCTTTTAC
1 TTTTACTCATTACCTTTTAC
15788 CATTATTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.21, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTACTCATTACCTTTTACTA
Found at i:15799 original size:20 final size:20
Alignment explanation
Indices: 15755--15822 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 20
15745 TTTTTACTGA
*
15755 TTACCTTTTACTATTTTACTCT
1 TTACCTTTTACCA--TTACTCT
*
15777 TTACCTTTTACCATTATTCT
1 TTACCTTTTACCATTACTCT
* *
15797 TTACTTTTTATCATTTTACTCT
1 TTACCTTTTACCA--TTACTCT
15819 TTAC
1 TTAC
15823 TAATTACTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
20 17 0.44
22 22 0.56
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (20 bp):
TTACCTTTTACCATTACTCT
Found at i:15806 original size:70 final size:70
Alignment explanation
Indices: 15675--15861 Score: 167
Period size: 70 Copynumber: 2.7 Consensus size: 70
15665 ACTATTTTAC
* *
15675 TTTTTACTGATTACCTTTTACTGATTACTATTTTACTCTTTACTGATTATCATTACCTTTTACCC
1 TTTTTACTGATTACCTTTTACTGATTACTACTTTACTCTTTACTCATTATCATTACCTTTTACCC
15740 CCTTT
66 CCTTT
* *
15745 TTTTTACTGATTACCTTTTACT-ATTTTACT-CTTTAC-CTTTTAC-CATTATTCTTTACTTTTT
1 TTTTTACTGATTACCTTTTACTGA--TTACTACTTTACTC-TTTACTCATTA-TCATTACCTTTT
* *
15806 A--TCATTT
62 ACCCCCTTT
* *
15813 TACTCTTTACTAATTA-CTTCTTACTGATTA-TTCTTTACTCTTTAC-CATT
1 T--T-TTTACTGATTACCTT-TTACTGATTACTACTTTACTCTTTACTCATT
15862 TTTCCTTTTA
Statistics
Matches: 99, Mismatches: 7, Indels: 22
0.77 0.05 0.17
Matches are distributed among these distances:
68 5 0.05
69 7 0.07
70 65 0.66
71 21 0.21
72 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.03, T:0.56
Consensus pattern (70 bp):
TTTTTACTGATTACCTTTTACTGATTACTACTTTACTCTTTACTCATTATCATTACCTTTTACCC
CCTTT
Found at i:15814 original size:50 final size:50
Alignment explanation
Indices: 15784--15880 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 50
15774 TCTTTACCTT
* *
15784 TTAC-CATTATTCTTTACTTTTTATCATTTTACTCTTTACTAATTACTTC
1 TTACTCATTATTCTTTACTCTTTACCATTTTACTCTTTACTAATTACTTC
* * *
15833 TTACTGATTATTCTTTACTCTTTACCATTTTTC-CTTTTACTGATTACT
1 TTACTCATTATTCTTTACTCTTTACCATTTTACTC-TTTACTAATTACT
15881 ATTTCACTCC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 5 0.12
50 36 0.88
ACGTcount: A:0.21, C:0.21, G:0.02, T:0.57
Consensus pattern (50 bp):
TTACTCATTATTCTTTACTCTTTACCATTTTACTCTTTACTAATTACTTC
Found at i:15850 original size:14 final size:15
Alignment explanation
Indices: 15812--15851 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
15802 TTTTATCATT
15812 TTAC-TCTTTACTAA
1 TTACTTCTTTACTAA
*
15826 TTACTTC-TTACTGA
1 TTACTTCTTTACTAA
15840 TTA-TTCTTTACT
1 TTACTTCTTTACT
15852 CTTTACCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 3 0.13
14 18 0.78
15 2 0.09
ACGTcount: A:0.23, C:0.20, G:0.03, T:0.55
Consensus pattern (15 bp):
TTACTTCTTTACTAA
Found at i:15941 original size:38 final size:38
Alignment explanation
Indices: 15867--16208 Score: 316
Period size: 38 Copynumber: 8.9 Consensus size: 38
15857 CCATTTTTCC
* *
15867 TTTTACTGATTACTATTTCACTCCCTTGATTATTAATTATTAA
1 TTTTACTGATTACTA-TT-ACT---TTGACTCTTAATTATTAA
* **
15910 TTTTACTGATTACTATTACTTTGACCCTTAATTATCGA
1 TTTTACTGATTACTATTACTTTGACTCTTAATTATTAA
* * * **
15948 TTTTACTGATTACTATCACTTTTACCCTTAATTATCGA
1 TTTTACTGATTACTATTACTTTGACTCTTAATTATTAA
* *
15986 TTTTACTGATTACTATTACTTTGATTCTCAATTACTTAA
1 TTTTACTGATTACTATTACTTTGACTCTTAATTA-TTAA
* *
16025 -TTCACTGATTACTATTACTTTGACTCTTAATT-TTCGA
1 TTTTACTGATTACTATTACTTTGACTCTTAATTATT-AA
* * *
16062 TTTTACTGATTACTATTACTCTGATTCTCAATTACTTAA
1 TTTTACTGATTACTATTACTTTGACTCTTAATTA-TTAA
* * *
16101 -TTCACTGATTACTGTTACTTTGACTCTTAATT-TTCGA
1 TTTTACTGATTACTATTACTTTGACTCTTAATTATT-AA
* * * * *
16138 TTTTATTGATTATTATTACTCTGATTCTCAATTACTTAA
1 TTTTACTGATTACTATTACTTTGACTCTTAATTA-TTAA
* *
16177 -TTCATTGATTACTATTACTTTGACTCTTAATT
1 TTTTACTGATTACTATTACTTTGACTCTTAATT
16209 TTATTGGGGT
Statistics
Matches: 248, Mismatches: 42, Indels: 23
0.79 0.13 0.07
Matches are distributed among these distances:
36 4 0.02
37 2 0.01
38 214 0.86
39 4 0.02
40 4 0.02
41 3 0.01
42 2 0.01
43 15 0.06
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.50
Consensus pattern (38 bp):
TTTTACTGATTACTATTACTTTGACTCTTAATTATTAA
Found at i:15970 original size:19 final size:19
Alignment explanation
Indices: 15948--16007 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
15938 TAATTATCGA
15948 TTTTACTGATTACTATCAC
1 TTTTACTGATTACTATCAC
** *
15967 TTTTAC-CCTTAATTATCGA-
1 TTTTACTGATT-ACTATC-AC
*
15986 TTTTACTGATTACTATTAC
1 TTTTACTGATTACTATCAC
16005 TTT
1 TTT
16008 GATTCTCAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 8
0.67 0.16 0.18
Matches are distributed among these distances:
18 3 0.10
19 24 0.80
20 3 0.10
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.52
Consensus pattern (19 bp):
TTTTACTGATTACTATCAC
Found at i:16209 original size:76 final size:76
Alignment explanation
Indices: 15909--16210 Score: 444
Period size: 76 Copynumber: 4.0 Consensus size: 76
15899 TTAATTATTA
* ** * * * * * *
15909 ATTTTACTGATTACTATTACTTTGACCCTTAATTA-TCGATTTTACTGATTACTATCACTTTTAC
1 ATTTTACTGATTACTATTACTCTGATTCTCAATTACT-TAATTCACTGATTACTATTACTTTGAC
* *
15973 CCTTAATTATCG
65 TCTTAATTTTCG
*
15985 ATTTTACTGATTACTATTACTTTGATTCTCAATTACTTAATTCACTGATTACTATTACTTTGACT
1 ATTTTACTGATTACTATTACTCTGATTCTCAATTACTTAATTCACTGATTACTATTACTTTGACT
16050 CTTAATTTTCG
66 CTTAATTTTCG
*
16061 ATTTTACTGATTACTATTACTCTGATTCTCAATTACTTAATTCACTGATTACTGTTACTTTGACT
1 ATTTTACTGATTACTATTACTCTGATTCTCAATTACTTAATTCACTGATTACTATTACTTTGACT
16126 CTTAATTTTCG
66 CTTAATTTTCG
* * *
16137 ATTTTATTGATTATTATTACTCTGATTCTCAATTACTTAATTCATTGATTACTATTACTTTGACT
1 ATTTTACTGATTACTATTACTCTGATTCTCAATTACTTAATTCACTGATTACTATTACTTTGACT
16202 CTTAATTTT
66 CTTAATTTT
16211 ATTGGGGTAC
Statistics
Matches: 209, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
76 208 1.00
77 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (76 bp):
ATTTTACTGATTACTATTACTCTGATTCTCAATTACTTAATTCACTGATTACTATTACTTTGACT
CTTAATTTTCG
Done.