Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007426.1 Corchorus capsularis cultivar CVL-1 contig07447, 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: 13506
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Found at i:4736 original size:32 final size:28
Alignment explanation
Indices: 4674--4757 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 28
4664 TATTACTAAT
*
4674 AAAGATTATGAACTCCGTTATAAAAAAA
1 AAAGATTATGAACTCCCTTATAAAAAAA
4702 AAAGATTATGAACTCCCTTGATGGCAAAAAAA
1 AAAGATTATGAACTCCCTT-AT---AAAAAAA
*
4734 AAAAATTATGAACTCCC-TATAAAA
1 AAAGATTATGAACTCCCTTATAAAA
4758 TCCACTAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
27 4 0.08
28 18 0.36
29 2 0.04
30 2 0.04
31 1 0.02
32 23 0.46
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAGATTATGAACTCCCTTATAAAAAAA
Found at i:5104 original size:20 final size:18
Alignment explanation
Indices: 5048--5103 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
5038 TTTCAGTTTG
*
5048 AATATAATACATA-T-AT
1 AATATATTACATATTAAT
5064 ATATATATTACATATTAAT
1 A-ATATATTACATATTAAT
*
5083 AATATATTATATATTAA-
1 AATATATTACATATTAAT
5100 AATA
1 AATA
5104 AAATTTTTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 1 0.03
17 15 0.43
18 16 0.46
19 3 0.09
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATATTACATATTAAT
Found at i:5146 original size:56 final size:57
Alignment explanation
Indices: 5055--5164 Score: 152
Period size: 56 Copynumber: 1.9 Consensus size: 57
5045 TTGAATATAA
* *
5055 TACATATATATATATATTACATATTAATAATATA-TTATATATTAAAATAAAATTTT
1 TACATATATATATATATTACATATTAATAAAATATTTACATATTAAAATAAAATTTT
* *
5111 TACATGTATATATATATT-CTTATTTAATAAAATATTTTACATATTAAAATAAAA
1 TACATATATATATATATTACATA-TTAATAAAATA-TTTACATATTAAAATAAAA
5165 ATGATTTTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
55 3 0.06
56 27 0.57
58 17 0.36
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (57 bp):
TACATATATATATATATTACATATTAATAAAATATTTACATATTAAAATAAAATTTT
Found at i:9970 original size:23 final size:23
Alignment explanation
Indices: 9938--9985 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
9928 AAAGCAAACA
*
9938 ATTATAAACTAACAATATTTCAG
1 ATTATAAACTAACAATATATCAG
*
9961 ATTATGAACTAACAATATATCAG
1 ATTATAAACTAACAATATATCAG
9984 AT
1 AT
9986 GATGCGGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (23 bp):
ATTATAAACTAACAATATATCAG
Found at i:11973 original size:17 final size:16
Alignment explanation
Indices: 11918--11973 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
11908 TTTCTTATTC
11918 TTTTACTTAATACCATT
1 TTTTAC-TAATACCATT
* *
11935 TTTCT-TTAATACCATC
1 TTT-TACTAATACCATT
*
11951 TCTTACTAGATACCATT
1 TTTTACTA-ATACCATT
11968 TTTTAC
1 TTTTAC
11974 CCTTAACACC
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 1 0.03
16 13 0.43
17 15 0.50
18 1 0.03
ACGTcount: A:0.27, C:0.21, G:0.02, T:0.50
Consensus pattern (16 bp):
TTTTACTAATACCATT
Found at i:12022 original size:16 final size:16
Alignment explanation
Indices: 11918--11989 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 16
11908 TTTCTTATTC
11918 TTTTACTTAATACCAT
1 TTTTACTTAATACCAT
11934 TTTT-CTTTAATACCAT
1 TTTTAC-TTAATACCAT
*
11950 CTCTTAC-TAGATACCATT
1 -TTTTACTTA-ATACCA-T
*
11968 TTTTACCCTTAACACCAT
1 TTTTA--CTTAATACCAT
11986 TTTT
1 TTTT
11990 TAATTCTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
15 1 0.02
16 16 0.36
17 13 0.29
18 7 0.16
19 6 0.13
20 2 0.04
ACGTcount: A:0.26, C:0.24, G:0.01, T:0.49
Consensus pattern (16 bp):
TTTTACTTAATACCAT
Found at i:12251 original size:14 final size:14
Alignment explanation
Indices: 12232--12258 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12222 TAGCGTTTTT
12232 TCTTTACTGATTAC
1 TCTTTACTGATTAC
12246 TCTTTACTGATTA
1 TCTTTACTGATTA
12259 GTACTGATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (14 bp):
TCTTTACTGATTAC
Found at i:12467 original size:32 final size:32
Alignment explanation
Indices: 12423--12487 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
12413 TTGGTCCTTC
12423 TTACTTCCTTTCTTAATTACTGATTAATCTTT
1 TTACTTCCTTTCTTAATTACTGATTAATCTTT
* *
12455 TTACTTCTTTTCTTAATTACTGATTACTCTTT
1 TTACTTCCTTTCTTAATTACTGATTAATCTTT
12487 T
1 T
12488 ACCCTCTCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.20, C:0.18, G:0.03, T:0.58
Consensus pattern (32 bp):
TTACTTCCTTTCTTAATTACTGATTAATCTTT
Found at i:12631 original size:38 final size:37
Alignment explanation
Indices: 12560--12672 Score: 145
Period size: 38 Copynumber: 3.0 Consensus size: 37
12550 ATTACTATTT
* *
12560 TTACCTTGACCCTTGATTATCAATTTTACTGATTACTA
1 TTACTTTGA-CCTTAATTATCAATTTTACTGATTACTA
* * * *
12598 TTACTTTGGTCCTTAATTATCAATTTTATTGATTATTC
1 TTACTTT-GACCTTAATTATCAATTTTACTGATTACTA
12636 TTACTTTGACTCTTAATTATCAATTTTACTGATTACT
1 TTACTTTGAC-CTTAATTATCAATTTTACTGATTACT
12673 TATCAATTTT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
37 2 0.03
38 61 0.95
39 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (37 bp):
TTACTTTGACCTTAATTATCAATTTTACTGATTACTA
Found at i:12681 original size:58 final size:58
Alignment explanation
Indices: 12614--12730 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
12604 TGGTCCTTAA
12614 TTATCAATTTTATTGATTATTCTTACTTTGACTCTTAATTATCAATTTTACTGATTAC
1 TTATCAATTTTATTGATTATTCTTACTTTGACTCTTAATTATCAATTTTACTGATTAC
12672 TTATCAATTTTATTGATTATTCTTACTTTGACTCTTAATTATCAATTTTACTGATTAC
1 TTATCAATTTTATTGATTATTCTTACTTTGACTCTTAATTATCAATTTTACTGATTAC
12730 T
1 T
12731 ATTACTTTGG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.27, C:0.14, G:0.05, T:0.54
Consensus pattern (58 bp):
TTATCAATTTTATTGATTATTCTTACTTTGACTCTTAATTATCAATTTTACTGATTAC
Found at i:12709 original size:96 final size:96
Alignment explanation
Indices: 12576--12766 Score: 278
Period size: 96 Copynumber: 2.0 Consensus size: 96
12566 TGACCCTTGA
* * * *
12576 TTATCAATTTTACTGATTACTATTACTTTGGTCCTTAATTATCAATTTTATTGATTATTCTTACT
1 TTATCAATTTTACTGATTACTATTACTTTGCTCCTTAATTATCAATTTTACTGATTACTATTACT
12641 TTGACT-CTTAATTATCAATTTTACTGATTAC
66 TTG-CTCCTTAATTATCAATTTTACTGATTAC
* * *
12672 TTATCAATTTTATTGATTATTCTTACTTTGACT-CTTAATTATCAATTTTACTGATTACTATTAC
1 TTATCAATTTTACTGATTACTATTACTTTG-CTCCTTAATTATCAATTTTACTGATTACTATTAC
*
12736 TTTGGTCCTTAATTATCAATTTTACTGATTA
65 TTTGCTCCTTAATTATCAATTTTACTGATTA
12767 TCCTTACTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
95 1 0.01
96 83 0.98
97 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.06, T:0.52
Consensus pattern (96 bp):
TTATCAATTTTACTGATTACTATTACTTTGCTCCTTAATTATCAATTTTACTGATTACTATTACT
TTGCTCCTTAATTATCAATTTTACTGATTAC
Found at i:12759 original size:76 final size:76
Alignment explanation
Indices: 12672--12825 Score: 290
Period size: 76 Copynumber: 2.0 Consensus size: 76
12662 TACTGATTAC
* *
12672 TTATCAATTTTATTGATTATTCTTACTTTGACTCTTAATTATCAATTTTACTGATTACTATTACT
1 TTATCAATTTTACTGATTATCCTTACTTTGACTCTTAATTATCAATTTTACTGATTACTATTACT
12737 TTGGTCCTTAA
66 TTGGTCCTTAA
12748 TTATCAATTTTACTGATTATCCTTACTTTGACTCTTAATTATCAATTTTACTGATTACTATTACT
1 TTATCAATTTTACTGATTATCCTTACTTTGACTCTTAATTATCAATTTTACTGATTACTATTACT
12813 TTGGTCCTTAA
66 TTGGTCCTTAA
12824 TT
1 TT
12826 TTACTGTGGT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (76 bp):
TTATCAATTTTACTGATTATCCTTACTTTGACTCTTAATTATCAATTTTACTGATTACTATTACT
TTGGTCCTTAA
Found at i:12805 original size:134 final size:134
Alignment explanation
Indices: 12555--12806 Score: 450
Period size: 134 Copynumber: 1.9 Consensus size: 134
12545 TACTAATTAC
* *
12555 TATTTTTACCTTGACCCTTGATTATCAATTTTACTGATTACTATTACTTTGGTCCTTAATTATCA
1 TATTCTTACCTTGACCCTTAATTATCAATTTTACTGATTACTATTACTTTGGTCCTTAATTATCA
* *
12620 ATTTTATTGATTATTCTTACTTTGACTCTTAATTATCAATTTTACTGATTACTTATCAATTTTAT
66 ATTTTACTGATTATCCTTACTTTGACTCTTAATTATCAATTTTACTGATTACTTATCAATTTTAT
12685 TGAT
131 TGAT
* *
12689 TATTCTTACTTTGACTCTTAATTATCAATTTTACTGATTACTATTACTTTGGTCCTTAATTATCA
1 TATTCTTACCTTGACCCTTAATTATCAATTTTACTGATTACTATTACTTTGGTCCTTAATTATCA
12754 ATTTTACTGATTATCCTTACTTTGACTCTTAATTATCAATTTTACTGATTACT
66 ATTTTACTGATTATCCTTACTTTGACTCTTAATTATCAATTTTACTGATTACT
12807 ATTACTTTGG
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
134 112 1.00
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (134 bp):
TATTCTTACCTTGACCCTTAATTATCAATTTTACTGATTACTATTACTTTGGTCCTTAATTATCA
ATTTTACTGATTATCCTTACTTTGACTCTTAATTATCAATTTTACTGATTACTTATCAATTTTAT
TGAT
Found at i:12825 original size:38 final size:38
Alignment explanation
Indices: 12672--12815 Score: 211
Period size: 38 Copynumber: 3.8 Consensus size: 38
12662 TACTGATTAC
* * *
12672 TTATCAATTTTATTGATTATTCTTACTTTGACTCTTAA
1 TTATCAATTTTACTGATTACTATTACTTTGACTCTTAA
*
12710 TTATCAATTTTACTGATTACTATTACTTTG-GTCCTTAA
1 TTATCAATTTTACTGATTACTATTACTTTGACT-CTTAA
*
12748 TTATCAATTTTACTGATTA-TCCTTACTTTGACTCTTAA
1 TTATCAATTTTACTGATTACT-ATTACTTTGACTCTTAA
12786 TTATCAATTTTACTGATTACTATTACTTTG
1 TTATCAATTTTACTGATTACTATTACTTTG
12816 GTCCTTAATT
Statistics
Matches: 95, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
37 2 0.02
38 91 0.96
39 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.52
Consensus pattern (38 bp):
TTATCAATTTTACTGATTACTATTACTTTGACTCTTAA
Done.