Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014977.1 Corchorus capsularis cultivar CVL-1 contig14998, 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: 11085
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Found at i:29 original size:16 final size:16
Alignment explanation
Indices: 8--60 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
1 TTTTTAA
*
8 TATATATTTTAATATT
1 TATATATATTAATATT
* * *
24 TATATAAAAT-ATAAT
1 TATATATATTAATATT
39 TATATATATTAATATT
1 TATATATATTAATATT
55 TATATA
1 TATATA
61 AATAAAAATA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATATATTAATATT
Found at i:47 original size:25 final size:25
Alignment explanation
Indices: 6--53 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1 TTTTT
* *
6 AATATATATTTTAATATTTATATAA
1 AATATATATTATAATATTAATATAA
31 AATATA-ATTATATATATTAATAT
1 AATATATATTATA-ATATTAATAT
54 TTATATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AATATATATTATAATATTAATATAA
Found at i:51 original size:31 final size:30
Alignment explanation
Indices: 5--96 Score: 109
Period size: 31 Copynumber: 3.1 Consensus size: 30
1 TTTT
*
5 TAATATATATTTTAATATTTATATAAAATA
1 TAATATATATATTAATATTTATATAAAATA
35 TAATTATATATATTAATATTTATAT-AAATA
1 TAA-TATATATATTAATATTTATATAAAATA
* * *
65 -AAAATATA-ATTATTATATATATAATAATA
1 TAATATATATATTAATATTTATATAA-AATA
94 TAA
1 TAA
97 ATGAACATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.22
28 6 0.11
29 6 0.11
30 10 0.19
31 20 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TAATATATATATTAATATTTATATAAAATA
Found at i:107 original size:41 final size:36
Alignment explanation
Indices: 29--107 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 36
19 ATATTTATAT
* *
29 AAAATATAATTATATATATTAATATTTATATAAATA
1 AAAATATAATTATATATATTAATATATAAATAAATA
65 AAAATATAATTATTATATATATAATAATATAAATGAACATA
1 AAAATATAATTA-TATATAT-TAAT-ATATAAAT-AA-ATA
106 AA
1 AA
108 CGAGCTATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
36 12 0.33
37 7 0.19
38 4 0.11
39 6 0.17
40 2 0.06
41 5 0.14
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (36 bp):
AAAATATAATTATATATATTAATATATAAATAAATA
Found at i:141 original size:11 final size:11
Alignment explanation
Indices: 93--158 Score: 53
Period size: 11 Copynumber: 6.0 Consensus size: 11
83 ATATAATAAT
*
93 ATAAATGAAC-
1 ATAAACGAACA
* *
103 ATAAACGAGCT
1 ATAAACGAACA
*
114 ATAAACGATCTA
1 ATAAACGAAC-A
*
126 TTAAACGAACA
1 ATAAACGAACA
*
137 ATAAACAAACA
1 ATAAACGAACA
*
148 CTAAACGAACA
1 ATAAACGAACA
159 TTAATCGAGC
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
10 8 0.18
11 28 0.64
12 8 0.18
ACGTcount: A:0.56, C:0.18, G:0.09, T:0.17
Consensus pattern (11 bp):
ATAAACGAACA
Found at i:841 original size:7 final size:7
Alignment explanation
Indices: 797--825 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
787 TTTGGCATCG
797 TTTCTGT
1 TTTCTGT
804 TTTCTGT
1 TTTCTGT
811 TTTCTGT
1 TTTCTGT
818 TTTCTGT
1 TTTCTGT
825 T
1 T
826 GCCAATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.72
Consensus pattern (7 bp):
TTTCTGT
Found at i:1124 original size:18 final size:18
Alignment explanation
Indices: 1104--1137 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1094 ACAGAGTAAA
1104 AAAACAAAAAC-GAAAAC
1 AAAACAAAAACAGAAAAC
1121 AAAACAAAAACAGAAAA
1 AAAACAAAAACAGAAAA
1138 ACGAAAACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.79, C:0.15, G:0.06, T:0.00
Consensus pattern (18 bp):
AAAACAAAAACAGAAAAC
Found at i:2806 original size:84 final size:77
Alignment explanation
Indices: 2642--2887 Score: 323
Period size: 78 Copynumber: 3.1 Consensus size: 77
2632 GTTTTTTAGT
*
2642 TAAAATAGTAAAATTTTAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAA-TATAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGA
* *
2707 TTTTTTAGTTGAG
65 GTTTTTAGTTAAG
*
2720 TAAAATAGTAAAATGATAAAATATAATAGTCATAAGGATTCACTCATTAGATTTAATTATATAAA
1 TAAAATAGTAAAAT-ATAAAATATAATAGTTATAAGG----A-T-ATTAGATTTAATTATATAAA
2785 AATAGAGTTTTTAGTTAAG
59 AATAGAGTTTTTAGTTAAG
* * * *
2804 TAAAATAGTAACATAGTAAAATAAAATAGTTATGAA-GATATTATATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATA-TAAAATATAATAGTTAT-AAGGATATTAGATTTAATTATATAAAAATAG
2868 AGTTTTTAGTTAAG
64 AGTTTTTAGTTAAG
2882 TAAAAT
1 TAAAAT
2888 TATAAAAACC
Statistics
Matches: 150, Mismatches: 9, Indels: 18
0.85 0.05 0.10
Matches are distributed among these distances:
77 1 0.01
78 76 0.51
79 1 0.01
80 1 0.01
82 1 0.01
83 2 0.01
84 66 0.44
85 2 0.01
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.37
Consensus pattern (77 bp):
TAAAATAGTAAAATATAAAATATAATAGTTATAAGGATATTAGATTTAATTATATAAAAATAGAG
TTTTTAGTTAAG
Found at i:3307 original size:3 final size:3
Alignment explanation
Indices: 3299--3345 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
3289 ATTAGTATAG
3299 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3346 ATTGAATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Done.