Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016133.1 Corchorus capsularis cultivar CVL-1 contig16154, 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: 19943
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2691 original size:6 final size:6
Alignment explanation
Indices: 2680--2707 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2670 CCCACCATTT
2680 CCTCAA CCTCAA CCTCAA CCTCAA CCTC
1 CCTCAA CCTCAA CCTCAA CCTCAA CCTC
2708 CCCCACCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.54, G:0.00, T:0.18
Consensus pattern (6 bp):
CCTCAA
Found at i:3192 original size:12 final size:12
Alignment explanation
Indices: 3175--3222 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
3165 TAAAAATATT
3175 GGGCTCGAGCTC
1 GGGCTCGAGCTC
3187 GGGCTCG-G-TC
1 GGGCTCGAGCTC
* *
3197 GAGCTCGGGCTC
1 GGGCTCGAGCTC
*
3209 GAGCTCGAGCTC
1 GGGCTCGAGCTC
3221 GG
1 GG
3223 TCGAGCTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 8 0.26
11 2 0.06
12 21 0.68
ACGTcount: A:0.08, C:0.31, G:0.44, T:0.17
Consensus pattern (12 bp):
GGGCTCGAGCTC
Found at i:3200 original size:16 final size:18
Alignment explanation
Indices: 3177--3222 Score: 78
Period size: 16 Copynumber: 2.7 Consensus size: 18
3167 AAAATATTGG
3177 GCTCGAGCTCGGGCTCG-
1 GCTCGAGCTCGGGCTCGA
3194 G-TCGAGCTCGGGCTCGA
1 GCTCGAGCTCGGGCTCGA
3211 GCTCGAGCTCGG
1 GCTCGAGCTCGG
3223 TCGAGCTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.56
17 2 0.07
18 10 0.37
ACGTcount: A:0.09, C:0.33, G:0.41, T:0.17
Consensus pattern (18 bp):
GCTCGAGCTCGGGCTCGA
Found at i:3204 original size:10 final size:11
Alignment explanation
Indices: 3176--3229 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
3166 AAAAATATTG
3176 GGCTCGAGCTC
1 GGCTCGAGCTC
3187 GGGCTCG-G-TC
1 -GGCTCGAGCTC
*
3197 GAGCTCGGGCTC
1 G-GCTCGAGCTC
3209 GAGCTCGAGCTC
1 G-GCTCGAGCTC
3221 GG-TCGAGCT
1 GGCTCGAGCT
3230 TTGTTTATGG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
9 1 0.03
10 14 0.37
11 3 0.08
12 20 0.53
ACGTcount: A:0.09, C:0.31, G:0.41, T:0.19
Consensus pattern (11 bp):
GGCTCGAGCTC
Found at i:3215 original size:28 final size:28
Alignment explanation
Indices: 3175--3229 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
3165 TAAAAATATT
*
3175 GGGCTCGAGCTCGGGCTCGGTCGAGCTC
1 GGGCTCGAGCTCGAGCTCGGTCGAGCTC
3203 GGGCTCGAGCTCGAGCTCGGTCGAGCT
1 GGGCTCGAGCTCGAGCTCGGTCGAGCT
3230 TTGTTTATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.09, C:0.31, G:0.42, T:0.18
Consensus pattern (28 bp):
GGGCTCGAGCTCGAGCTCGGTCGAGCTC
Found at i:3226 original size:16 final size:15
Alignment explanation
Indices: 3179--3229 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
3169 AATATTGGGC
3179 TCGAGCTCGGGCTCGG
1 TCGAGCTC-GGCTCGG
*
3195 TCGAGCTCGG---GC
1 TCGAGCTCGGCTCGG
3207 TCGAGCTCGAGCTCGG
1 TCGAGCTCG-GCTCGG
3223 TCGAGCT
1 TCGAGCT
3230 TTGTTTATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 10 0.34
13 1 0.03
15 2 0.07
16 16 0.55
ACGTcount: A:0.10, C:0.31, G:0.39, T:0.20
Consensus pattern (15 bp):
TCGAGCTCGGCTCGG
Found at i:4881 original size:23 final size:22
Alignment explanation
Indices: 4850--4929 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 22
4840 ATTTTTATTG
4850 ATAT-TATATTGATAATATATAT
1 ATATATATATTGATAATAT-TAT
4872 ATATATATATTGATAATATT-T
1 ATATATATATTGATAATATTAT
* * * *
4893 TTTTACTATAAATGATGATATTAT
1 ATATA-TAT-ATTGATAATATTAT
*
4917 ATTTATATATTGA
1 ATATATATATTGA
4930 CACCACTGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
21 4 0.08
22 12 0.25
23 27 0.56
24 5 0.10
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.51
Consensus pattern (22 bp):
ATATATATATTGATAATATTAT
Found at i:9451 original size:13 final size:14
Alignment explanation
Indices: 9428--9456 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
9418 ACTTCTATTT
9428 AATGCATGGATGCA
1 AATGCATGGATGCA
9442 AATG-ATGGATGCA
1 AATGCATGGATGCA
9455 AA
1 AA
9457 GTCCAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.21
Consensus pattern (14 bp):
AATGCATGGATGCA
Found at i:12569 original size:28 final size:28
Alignment explanation
Indices: 12537--12609 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
12527 GTAGATTAAG
*
12537 AATGACCAAAATATCCCCTAAATGCAAA
1 AATGACCAAAATACCCCCTAAATGCAAA
* **
12565 AATGACCAAAATGCCCCCTAAATGTGAA
1 AATGACCAAAATACCCCCTAAATGCAAA
*
12593 AATGACCAAAATGCCCC
1 AATGACCAAAATACCCC
12610 TAGATGACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.45, C:0.27, G:0.11, T:0.16
Consensus pattern (28 bp):
AATGACCAAAATACCCCCTAAATGCAAA
Found at i:14021 original size:12 final size:11
Alignment explanation
Indices: 14004--14044 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
13994 AGGAATAACA
14004 TCTTCTTCTTCT
1 TCTTCTT-TTCT
*
14016 TCTTCTTTTTT
1 TCTTCTTTTCT
14027 TCTT-TTTTCT
1 TCTTCTTTTCT
14037 T-TTCTTTT
1 TCTTCTTTT
14045 TTTTGTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 2 0.08
10 10 0.38
11 7 0.27
12 7 0.27
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TCTTCTTTTCT
Found at i:14041 original size:23 final size:24
Alignment explanation
Indices: 14009--14055 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
13999 TAACATCTTC
14009 TTCTTCTTCTTCTTTTTT-TCTTTT
1 TTCTTCTTCTT-TTTTTTGTCTTTT
14033 TTCTT-TTCTTTTTTTTGTCTTTT
1 TTCTTCTTCTTTTTTTTGTCTTTT
14056 ACTTTGATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 11 0.50
24 5 0.23
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (24 bp):
TTCTTCTTCTTTTTTTTGTCTTTT
Found at i:14053 original size:16 final size:16
Alignment explanation
Indices: 14018--14060 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
14008 CTTCTTCTTC
14018 TTCTTTT-TTTCTTTT
1 TTCTTTTCTTTCTTTT
14033 TTCTTTTCTTT-TTTT
1 TTCTTTTCTTTCTTTT
14048 TGTCTTTTACTTT
1 T-TCTTTT-CTTT
14061 GATGGAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 12 0.48
16 9 0.36
17 4 0.16
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (16 bp):
TTCTTTTCTTTCTTTT
Done.