Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007896.1 Corchorus capsularis cultivar CVL-1 contig07917, 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: 11450
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:1988 original size:102 final size:101
Alignment explanation
Indices: 1784--2088 Score: 398
Period size: 102 Copynumber: 3.0 Consensus size: 101
1774 CGGATTTTTC
* * * *
1784 TGTAGTAATTTCCGTTGGAACAAATT-TTTTTGGCGCAAAATATTTCGGCTAGCGGGAATTCGAA
1 TGTAGTAATTTCCGTTGCAA-AAATTAATTTTGGCGCAAAATATTTAGG--AGCGGGAATTCAAA
* *
1848 TTTTAATTTGTCACGAAAGTTAAAATCGTTGCAAAATTT
63 TTTTAATTTGTCACGAAAATTAAATTCGTTGCAAAATTT
*
1887 TGTAGTAATTTCCGTTGCAAAAATTAATTTTGGCGCAAAATATTTAAGGAGCGGGAATTCAAAAT
1 TGTAGTAATTTCCGTTGCAAAAATTAATTTTGGCGCAAAATATTT-AGGAGCGGGAATTCAAATT
* * *
1952 TTAATTTGTTATGAAAACTAAATTCGTTGCAAAATTT
65 TTAATTTGTCACGAAAATTAAATTCGTTGCAAAATTT
* * *
1989 CGTAATAATTT-CGTTGCAAAAATTAATTTTGGCGCAAAATTTTTGAGCGAGCGGGAATTCAAAT
1 TGTAGTAATTTCCGTTGCAAAAATTAATTTTGGCGCAAAATATTT-AG-GAGCGGGAATTCAAAT
* * *
2053 TTTAATTTGCCACGAAAATTAATTTCGTGGCAAAAT
64 TTTAATTTGTCACGAAAATTAAATTCGTTGCAAAAT
2089 CTGTAGCAAA
Statistics
Matches: 178, Mismatches: 21, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
101 34 0.19
102 105 0.59
103 37 0.21
104 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (101 bp):
TGTAGTAATTTCCGTTGCAAAAATTAATTTTGGCGCAAAATATTTAGGAGCGGGAATTCAAATTT
TAATTTGTCACGAAAATTAAATTCGTTGCAAAATTT
Found at i:2860 original size:2 final size:2
Alignment explanation
Indices: 2853--2882 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2843 GTGGGTGACA
2853 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
2883 CTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4689 original size:15 final size:15
Alignment explanation
Indices: 4668--4705 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4658 TAAGGTAATA
4668 ATAATAATT-TTACT
1 ATAATAATTATTACT
*
4682 ACTAATAATTATTATT
1 A-TAATAATTATTACT
4698 ATAATAAT
1 ATAATAAT
4706 AAGAAGTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 15 0.71
16 5 0.24
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAATAATTATTACT
Found at i:4705 original size:18 final size:18
Alignment explanation
Indices: 4663--4707 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
4653 AAGATTAAGG
4663 TAATAATAATAATTTTAC
1 TAATAATAATAATTTTAC
* *
4681 TACTAATAATTATTATTA-
1 TAATAATAATAATT-TTAC
4699 TAATAATAA
1 TAATAATAA
4708 GAAGTTTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATAATAATAATTTTAC
Found at i:5138 original size:90 final size:89
Alignment explanation
Indices: 5027--5302 Score: 403
Period size: 90 Copynumber: 3.1 Consensus size: 89
5017 GGATATTCCA
*
5027 TATA-ATTAATCCTTAAAAATTTAACTAAAACTAAAAATTAAAAAGGGTATTTTAAATATTTATG
1 TATAGATTAATCCTTAAAAATTTAACTAAAATTAAAAATTAAAAAGGGTATTTTAAATATTTA-G
5091 GTCAAAGGTTTTTGAAGTTTAGGAT
65 GTCAAAGGTTTTTGAAGTTTAGGAT
*
5116 TATAGATTAATCCTTAAAAATTTAACTAAAATTAAAAATTAAAAAGGGTATTTTAAATATATAAG
1 TATAGATTAATCCTTAAAAATTTAACTAAAATTAAAAATTAAAAAGGGTATTTTAAATAT-TTAG
* *
5181 ATCAAAGGTTTTTTAAGTTTAGGAT
65 GTCAAAGGTTTTTGAAGTTTAGGAT
* * *
5206 TATAGATTAATCCTTAAAAATATAACTAAAATTAAAAATTAAAAAGAGTATTTTAGATATTTCAG
1 TATAGATTAATCCTTAAAAATTTAACTAAAATTAAAAATTAAAAAGGGTATTTTAAATATTT-AG
* * *
5271 GTTC-ACGATTTTTTGAAGTTTAGAAT
65 G-TCAAAG-GTTTTTGAAGTTTAGGAT
5297 TATAGA
1 TATAGA
5303 GTATAAAGAT
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
89 5 0.03
90 139 0.82
91 25 0.15
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (89 bp):
TATAGATTAATCCTTAAAAATTTAACTAAAATTAAAAATTAAAAAGGGTATTTTAAATATTTAGG
TCAAAGGTTTTTGAAGTTTAGGAT
Found at i:5324 original size:2 final size:2
Alignment explanation
Indices: 5317--5353 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5307 AAAGATAAAG
5317 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5354 AAACTCAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6965 original size:25 final size:25
Alignment explanation
Indices: 6931--6981 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
6921 GCCCAACCAA
6931 GAAGCACACAGCCCAAAAAAATTAG
1 GAAGCACACAGCCCAAAAAAATTAG
*
6956 GAAGCCCACAGCCCAAAAAAATTAG
1 GAAGCACACAGCCCAAAAAAATTAG
6981 G
1 G
6982 TGAATAGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.49, C:0.25, G:0.18, T:0.08
Consensus pattern (25 bp):
GAAGCACACAGCCCAAAAAAATTAG
Found at i:9484 original size:13 final size:13
Alignment explanation
Indices: 9466--9491 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9456 TTTTAATATA
9466 GATATTTGTGAGT
1 GATATTTGTGAGT
9479 GATATTTGTGAGT
1 GATATTTGTGAGT
9492 CGCCGAGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (13 bp):
GATATTTGTGAGT
Found at i:10759 original size:25 final size:26
Alignment explanation
Indices: 10713--10774 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 26
10703 TCTTACCGAT
*
10713 TACCATTTTTGCTTTTGCTAC-TGAA
1 TACCATTTTTACTTTTGCTACTTGAA
**
10738 TACCATTTTTACTTTTTTTACTATTGAA
1 TACCATTTTTACTTTTGCTAC--TTGAA
10766 TACCATTTT
1 TACCATTTT
10775 GATCCTTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.58
28 13 0.42
ACGTcount: A:0.23, C:0.18, G:0.06, T:0.53
Consensus pattern (26 bp):
TACCATTTTTACTTTTGCTACTTGAA
Found at i:10877 original size:7 final size:7
Alignment explanation
Indices: 10856--11005 Score: 65
Period size: 7 Copynumber: 20.4 Consensus size: 7
10846 TGCCATTTTT
10856 CTCTTTA
1 CTCTTTA
**
10863 CTGATTA
1 CTCTTTA
10870 CTCTTTA
1 CTCTTTA
*
10877 CCCTTTTA
1 CTC-TTTA
10885 C-CATTTTA
1 CTC--TTTA
10893 CTCTTTTA
1 CTC-TTTA
**
10901 CTGATTA
1 CTCTTTA
10908 CTCTTTA
1 CTCTTTA
*
10915 CTTTTTA
1 CTCTTTA
10922 C-CATTTTA
1 CTC--TTTA
10930 CTCTTTA
1 CTCTTTA
**
10937 CTGATTA
1 CTCTTTA
10944 CTCTTTA
1 CTCTTTA
*
10951 CTTTTTA
1 CTCTTTA
10958 -TCATCTTA
1 CTC-T-TTA
10966 CTCTTTA
1 CTCTTTA
*
10973 CTATTTTA
1 CT-CTTTA
**
10981 CTGATTA
1 CTCTTTA
10988 CTTCTTTTA
1 C-TC-TTTA
10997 CTC-TTA
1 CTCTTTA
11003 CTC
1 CTC
11006 ATAATTACCA
Statistics
Matches: 109, Mismatches: 22, Indels: 25
0.70 0.14 0.16
Matches are distributed among these distances:
6 7 0.06
7 58 0.53
8 36 0.33
9 8 0.07
ACGTcount: A:0.19, C:0.24, G:0.03, T:0.55
Consensus pattern (7 bp):
CTCTTTA
Found at i:10937 original size:36 final size:36
Alignment explanation
Indices: 10842--10974 Score: 203
Period size: 36 Copynumber: 3.6 Consensus size: 36
10832 TTATTATATT
* *
10842 TTTTTGCCATTTTTCTCTTTACTGATTACTCTTTACC
1 TTTTTACCATTTTACTCTTTACTGATTACTCTTTA-C
*
10879 CTTTTACCATTTTACTCTTTTACTGATTACTCTTTAC
1 TTTTTACCATTTTACTC-TTTACTGATTACTCTTTAC
10916 TTTTTACCATTTTACTCTTTACTGATTACTCTTTAC
1 TTTTTACCATTTTACTCTTTACTGATTACTCTTTAC
* *
10952 TTTTTATCATCTTACTCTTTACT
1 TTTTTACCATTTTACTCTTTACT
10975 ATTTTACTGA
Statistics
Matches: 89, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
36 40 0.45
37 31 0.35
38 18 0.20
ACGTcount: A:0.17, C:0.23, G:0.03, T:0.56
Consensus pattern (36 bp):
TTTTTACCATTTTACTCTTTACTGATTACTCTTTAC
Found at i:10988 original size:22 final size:21
Alignment explanation
Indices: 10926--10994 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 21
10916 TTTTTACCAT
*
10926 TTTACTCTTTACTGATTACTC
1 TTTACTTTTTACTGATTACTC
*
10947 TTTACTTTTTATCAT-CTTACTC
1 TTTACTTTTTA-C-TGATTACTC
10969 TTTACTATTTTACTGATTACTTC
1 TTTACT-TTTTACTGATTAC-TC
10992 TTT
1 TTT
10995 TACTCTTACT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
21 11 0.28
22 18 0.45
23 11 0.28
ACGTcount: A:0.19, C:0.20, G:0.03, T:0.58
Consensus pattern (21 bp):
TTTACTTTTTACTGATTACTC
Found at i:11037 original size:16 final size:16
Alignment explanation
Indices: 11016--11079 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 16
11006 ATAATTACCA
11016 TTTTACTGATTACTTC
1 TTTTACTGATTACTTC
** *
11032 TTTTACT--TTTGTCCC
1 TTTTACTGATTACT-TC
11047 TTTTACTGATTACTTC
1 TTTTACTGATTACTTC
* *
11063 CTTTACTGATTATTTC
1 TTTTACTGATTACTTC
11079 T
1 T
11080 CTTGATTGCC
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
14 3 0.08
15 8 0.22
16 22 0.61
17 3 0.08
ACGTcount: A:0.16, C:0.20, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTTACTGATTACTTC
Done.