Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016260.1 Corchorus capsularis cultivar CVL-1 contig16281, 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: 24271
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--38 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1 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
39 GTAATTTACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6065 original size:9 final size:9
Alignment explanation
Indices: 6047--6083 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
6037 GTTCTGGCCA
6047 AAAG-AAAG
1 AAAGAAAAG
6055 AAAGAAAAG
1 AAAGAAAAG
*
6064 AAAAAAAAG
1 AAAGAAAAG
6073 AAAGAAAAG
1 AAAGAAAAG
6082 AA
1 AA
6084 CTAAATCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 4 0.15
9 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:6072 original size:18 final size:18
Alignment explanation
Indices: 6046--6083 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
6036 CGTTCTGGCC
*
6046 AAAAGAAAGAAAGAAAAG
1 AAAAAAAAGAAAGAAAAG
6064 AAAAAAAAGAAAGAAAAG
1 AAAAAAAAGAAAGAAAAG
6082 AA
1 AA
6084 CTAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAGAAAAG
Found at i:11682 original size:31 final size:31
Alignment explanation
Indices: 11644--11706 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
11634 GAGGCTATGG
*
11644 TGTGCAAATATTGATCTTAAATTGGATTCTT
1 TGTGCAAATATTGACCTTAAATTGGATTCTT
11675 TGTGCAAATATTGACCTTAAATTGGATTCTT
1 TGTGCAAATATTGACCTTAAATTGGATTCTT
11706 T
1 T
11707 TTAAGGATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (31 bp):
TGTGCAAATATTGACCTTAAATTGGATTCTT
Found at i:15957 original size:2 final size:2
Alignment explanation
Indices: 15950--15999 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
15940 TAAATGTTAA
* *
15950 AT AT AT AT TT GT AT AT AT AT -T AT AT A- 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
15990 AT AT AT AT AT
1 AT AT AT AT AT
16000 TACTTGTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:15990 original size:36 final size:36
Alignment explanation
Indices: 15924--15993 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
15914 ATCTTTCAAA
*
15924 GTATATAAATTATAAATAAATGTTAAATATATATTT
1 GTATATAAATTATAAATAAATGATAAATATATATTT
* * *
15960 GTATATATATTATATAATATAT-ATATATATATAT
1 GTATATAAATTATA-AATAAATGATAAATATATAT
15994 ATATATTACT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 23 0.79
37 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (36 bp):
GTATATAAATTATAAATAAATGATAAATATATATTT
Found at i:22567 original size:16 final size:18
Alignment explanation
Indices: 22540--22574 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
22530 GTATCTCCTG
22540 TTTCACTGCCCCT-TTTT
1 TTTCACTGCCCCTGTTTT
22557 TTTCA-TGCCCCTGTTTT
1 TTTCACTGCCCCTGTTTT
22574 T
1 T
22575 ATTTCCTCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.06, C:0.31, G:0.09, T:0.54
Consensus pattern (18 bp):
TTTCACTGCCCCTGTTTT
Done.