Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012348.1 Corchorus olitorius cultivar O-4 contig12381, 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: 21786
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Found at i:2122 original size:22 final size:22
Alignment explanation
Indices: 2094--2136 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2084 GTTATACCAA
2094 TCTTCTTATTCAAGGTTACTAT
1 TCTTCTTATTCAAGGTTACTAT
*
2116 TCTTCTTATTCAAGTTTACTA
1 TCTTCTTATTCAAGGTTACTA
2137 AAAAAAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.19, G:0.07, T:0.51
Consensus pattern (22 bp):
TCTTCTTATTCAAGGTTACTAT
Found at i:2607 original size:16 final size:16
Alignment explanation
Indices: 2586--2617 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2576 TATATATAAA
2586 GTATATATAAACTACT
1 GTATATATAAACTACT
2602 GTATATATAAACTACT
1 GTATATATAAACTACT
2618 ATCTCCCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
GTATATATAAACTACT
Found at i:5531 original size:12 final size:12
Alignment explanation
Indices: 5501--5545 Score: 63
Period size: 12 Copynumber: 3.5 Consensus size: 12
5491 TCATGCACCC
5501 AAAACAATTTATTT
1 AAAACAATTTA--T
5515 AAAACAATTTAT
1 AAAACAATTTAT
5527 AAAACAATTTAAT
1 AAAACAATTT-AT
5540 AAAACA
1 AAAACA
5546 GTAATAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.37
13 8 0.27
14 11 0.37
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAACAATTTAT
Found at i:7868 original size:24 final size:24
Alignment explanation
Indices: 7836--7882 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
7826 AGTAAAAATA
7836 CAATTTAGCTCTCCCATGCACACC
1 CAATTTAGCTCTCCCATGCACACC
7860 CAATTTAGCTCTCCCATGCACAC
1 CAATTTAGCTCTCCCATGCACAC
7883 GCCGAACTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.40, G:0.09, T:0.26
Consensus pattern (24 bp):
CAATTTAGCTCTCCCATGCACACC
Found at i:8338 original size:26 final size:26
Alignment explanation
Indices: 8296--8347 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
8286 AGAAAATCGT
* *
8296 TAAAACCAATATCATAATCAAAATCA
1 TAAAACCAATATAATAAACAAAATCA
*
8322 TAAAACCAA-AGTAATAAACCAAATCA
1 TAAAACCAATA-TAATAAACAAAATCA
8348 GTCAAATTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.60, C:0.19, G:0.02, T:0.19
Consensus pattern (26 bp):
TAAAACCAATATAATAAACAAAATCA
Found at i:9406 original size:16 final size:16
Alignment explanation
Indices: 9357--9452 Score: 70
Period size: 16 Copynumber: 5.8 Consensus size: 16
9347 CAAATTTTCC
9357 TTTTTATTTCCTTATTTA
1 TTTTT-TTTCCTT-TTTA
* **
9375 TTATTTTTATTATTTTA
1 TTTTTTTTCCT-TTTTA
9392 TTTTTTTTCC-TTTT-
1 TTTTTTTTCCTTTTTA
* *
9406 TTCTTTTTCCTTTTTC
1 TTTTTTTTCCTTTTTA
* *
9422 TTTTTTTTTCTTTTTC
1 TTTTTTTTCCTTTTTA
9438 TTTCTCTTTTCCTTT
1 TTT-T-TTTTCCTTT
9453 CTTTTCTTGG
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
14 9 0.14
15 8 0.13
16 17 0.27
17 16 0.25
18 13 0.21
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTTTCCTTTTTA
Found at i:9412 original size:14 final size:13
Alignment explanation
Indices: 9395--9452 Score: 63
Period size: 12 Copynumber: 4.8 Consensus size: 13
9385 TATTTTATTT
9395 TTTTTCCTTTTTTC
1 TTTTTCC-TTTTTC
9409 TTTTTCCTTTTTC
1 TTTTTCCTTTTTC
9422 -TTTT--TTTTTC
1 TTTTTCCTTTTTC
*
9432 TTTTT-CTTTCTC
1 TTTTTCCTTTTTC
9444 -TTTTCCTTT
1 TTTTTCCTTT
9453 CTTTTCTTGG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
10 6 0.15
11 8 0.20
12 13 0.32
13 6 0.15
14 7 0.17
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTCCTTTTTC
Found at i:9440 original size:22 final size:23
Alignment explanation
Indices: 9402--9457 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
9392 TTTTTTTTCC
*
9402 TTTTTTCTTTTTCCTTTTTCTTT
1 TTTTTTCTTTTTCCTTTCTCTTT
9425 TTTTTTCTTTTT-CTTTCTCTTT
1 TTTTTTCTTTTTCCTTTCTCTTT
**
9447 TCCTTTCTTTT
1 TTTTTTCTTTT
9458 CTTGGCTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 18 0.60
23 12 0.40
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTCTTTTTCCTTTCTCTTT
Found at i:9455 original size:10 final size:10
Alignment explanation
Indices: 9417--9460 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
9407 TCTTTTTCCT
*
9417 TTTTCTTTTT
1 TTTTCTTTTC
9427 TTTTCTTTTTC
1 TTTTC-TTTTC
9438 TTTCTCTTTTC
1 TTT-TCTTTTC
*
9449 CTTTCTTTTC
1 TTTTCTTTTC
9459 TT
1 TT
9461 GGCTTGGGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 13 0.45
11 14 0.48
12 2 0.07
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTCTTTTC
Found at i:14681 original size:14 final size:14
Alignment explanation
Indices: 14662--14706 Score: 60
Period size: 12 Copynumber: 3.4 Consensus size: 14
14652 TCACGCACCC
*
14662 AAAACAATTTATTT
1 AAAACAATTTATAT
14676 AAAACAA--TATAT
1 AAAACAATTTATAT
14688 AAAACAATTTA-AT
1 AAAACAATTTATAT
14701 AAAACA
1 AAAACA
14707 GTAATAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 11 0.39
13 8 0.29
14 9 0.32
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAACAATTTATAT
Found at i:14698 original size:26 final size:24
Alignment explanation
Indices: 14662--14715 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 24
14652 TCACGCACCC
*
14662 AAAACAATTTATTTAAAACAATATAT
1 AAAACAATTTA-ATAAAACAATA-AT
*
14688 AAAACAATTTAATAAAACAGTAAT
1 AAAACAATTTAATAAAACAATAAT
14712 AAAA
1 AAAA
14716 TAGTTCCCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 6 0.23
25 9 0.35
26 11 0.42
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAACAATTTAATAAAACAATAAT
Found at i:16070 original size:2 final size:2
Alignment explanation
Indices: 16063--16088 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16053 CGGTTAGCCC
16063 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
16089 GGGCTAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.