Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015459.1 Corchorus capsularis cultivar CVL-1 contig15480, 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: 7192
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Found at i:185 original size:26 final size:28
Alignment explanation
Indices: 150--232 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 28
140 TTAGAAGTAA
*
150 AGAGTAAAAAGTGGTATTTAGTAAAAAGG
1 AGAGTAAAAA-TGGTATTGAGTAAAAAGG
179 -G-GTAAAAATGGTATTGAGTAAAAAGG
1 AGAGTAAAAATGGTATTGAGTAAAAAGG
*
205 AGAGTAAAAAAATGGTAATTAAGTAAAA
1 AGAGT--AAAAATGGT-ATTGAGTAAAA
233 GGACTAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
26 17 0.36
27 8 0.17
28 3 0.06
30 9 0.19
31 10 0.21
ACGTcount: A:0.52, C:0.00, G:0.25, T:0.23
Consensus pattern (28 bp):
AGAGTAAAAATGGTATTGAGTAAAAAGG
Found at i:230 original size:57 final size:55
Alignment explanation
Indices: 150--307 Score: 155
Period size: 56 Copynumber: 2.9 Consensus size: 55
140 TTAGAAGTAA
* * * * * *
150 AGAGT-AAAAAGTGGTATTTAGTAAAAAGGGGTAAAAATGGTATTGAGTAAAAAGG
1 AGAGTAAAAAAATGGTAATTAGTAAAAAGGAGTAAAAATGGTATTCAGCAAAAA-C
*
205 AGAGTAAAAAAATGGTAATTAAGT-AAAAGGACTAAAAAGTGGTATTCAGCAAAAAC
1 AGAGTAAAAAAATGGTAATT-AGTAAAAAGGAGTAAAAA-TGGTATTCAGCAAAAAC
* *
261 AGA--AAGAAAATGGGTAATTAGTAAAAA-GAGTAAAATATGGTAATCAG
1 AGAGTAAAAAAAT-GGTAATTAGTAAAAAGGAGTAAAA-ATGGTATTCAG
308 TAATTCAAAG
Statistics
Matches: 87, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
54 26 0.30
55 17 0.20
56 27 0.31
57 17 0.20
ACGTcount: A:0.51, C:0.03, G:0.24, T:0.22
Consensus pattern (55 bp):
AGAGTAAAAAAATGGTAATTAGTAAAAAGGAGTAAAAATGGTATTCAGCAAAAAC
Found at i:300 original size:27 final size:26
Alignment explanation
Indices: 118--310 Score: 80
Period size: 26 Copynumber: 7.1 Consensus size: 26
108 GCAAGTAAGA
* *
118 TAAACAGAGTAAAAGA-GAGTAATTAG
1 TAAAAAGAGTAAAA-ATGGGTAATTAG
*
144 -AAGTAAAGAGTAAAAA-GTGGTATTTAG
1 TAA--AAAGAGTAAAAATG-GGTAATTAG
*
171 TAAAAAGGGGTAAAAAT-GGT-ATTGAG
1 TAAAAA-GAGTAAAAATGGGTAATT-AG
197 TAAAAAGGAGAGTAAAAAAAT-GGTAATTAAG
1 T-AAAA--AGAGT--AAAAATGGGTAATT-AG
* *
228 TAAAAGGACTAAAAA-GTGGT-ATTCAG
1 TAAAAAGAGTAAAAATG-GGTAATT-AG
* * *
254 CAAAAACAGAAAGAAAATGGGTAATTAG
1 TAAAAAGAG-TA-AAAATGGGTAATTAG
*
282 TAAAAAGAGTAAAATAT-GGTAATCAG
1 TAAAAAGAGTAAAA-ATGGGTAATTAG
308 TAA
1 TAA
311 TTCAAAGAGT
Statistics
Matches: 128, Mismatches: 19, Indels: 40
0.68 0.10 0.21
Matches are distributed among these distances:
25 4 0.03
26 40 0.31
27 36 0.28
28 24 0.19
29 5 0.04
30 13 0.10
31 6 0.05
ACGTcount: A:0.52, C:0.03, G:0.23, T:0.21
Consensus pattern (26 bp):
TAAAAAGAGTAAAAATGGGTAATTAG
Found at i:302 original size:54 final size:54
Alignment explanation
Indices: 150--307 Score: 149
Period size: 54 Copynumber: 2.9 Consensus size: 54
140 TTAGAAGTAA
* * * * * * *
150 AGAGTAAAAAGTGGTATTTAGTAAAAAGGGGTAAAAATGGTATTGAGTAAAAAGG
1 AGAGAAAAAAATGGTAATTAGTAAAAA-GAGTAAAAATGGTATTCAGCAAAAAGC
* *
205 AGAGTAAAAAAATGGTAATTAAGTAAAAGGACTAAAAAGTGGTATTCAGCAAAAA-C
1 AGAG-AAAAAAATGGTAATT-AGTAAAAAGAGTAAAAA-TGGTATTCAGCAAAAAGC
* *
261 AGA-AAGAAAATGGGTAATTAGTAAAAAGAGTAAAATATGGTAATCAG
1 AGAGAAAAAAAT-GGTAATTAGTAAAAAGAGTAAAA-ATGGTATTCAG
308 TAATTCAAAG
Statistics
Matches: 85, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
54 30 0.35
55 12 0.14
56 22 0.26
57 21 0.25
ACGTcount: A:0.51, C:0.03, G:0.24, T:0.22
Consensus pattern (54 bp):
AGAGAAAAAAATGGTAATTAGTAAAAAGAGTAAAAATGGTATTCAGCAAAAAGC
Found at i:309 original size:26 final size:25
Alignment explanation
Indices: 148--336 Score: 92
Period size: 26 Copynumber: 7.0 Consensus size: 25
138 AATTAGAAGT
* *
148 AAAGAGTAAAAAGTGGTATTTAGTAA
1 AAAGAGTAAAAA-TGGTAATCAGTAA
* * *
174 AAAGGGGTAAAAATGGTATTGAGTAAA
1 AAA-GAGTAAAAATGGTAATCAGT-AA
*
201 AAGGAGAGTAAAAAAATGGTAATTAAGTAA
1 AA--AGAGT--AAAAATGGTAA-TCAGTAA
* * * *
231 AAGGACTAAAAAGTGGTATTCAGCAA
1 AAAGAGTAAAAA-TGGTAATCAGTAA
* * *
257 AAACAGAAAGAAAATGGGTAATTAGTAA
1 AAAGAG-TA-AAAAT-GGTAATCAGTAA
285 AAAGAGTAAAATATGGTAATCAGTAA
1 AAAGAGTAAAA-ATGGTAATCAGTAA
* *
311 TTCAAAGAGT-AAGATGGTAGTCAGTA
1 ---AAAGAGTAAAAATGGTAATCAGTA
337 TAAGAAAAGG
Statistics
Matches: 126, Mismatches: 22, Indels: 29
0.71 0.12 0.16
Matches are distributed among these distances:
26 40 0.32
27 34 0.27
28 26 0.21
29 8 0.06
30 14 0.11
31 4 0.03
ACGTcount: A:0.50, C:0.04, G:0.24, T:0.22
Consensus pattern (25 bp):
AAAGAGTAAAAATGGTAATCAGTAA
Found at i:386 original size:29 final size:28
Alignment explanation
Indices: 361--426 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 28
351 GTAAAAAGTG
361 GTAATAAATAAAAGAGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
**
389 GTAATTGATAAAA-AGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
*
416 GTAAAAAATAA
1 GTAATAAATAA
427 TAAAAGTAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
27 22 0.67
28 11 0.33
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.17
Consensus pattern (28 bp):
GTAATAAATAAAAGAGAGTAAGAAAAGA
Found at i:426 original size:27 final size:27
Alignment explanation
Indices: 361--434 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
351 GTAAAAAGTG
361 GTAATAAATAAAAGAGAGTAAGAAAAGA
1 GTAATAAATAAAA-AGAGTAAGAAAAGA
**
389 GTAATTGATAAAAAGAGTAAGAAAAGA
1 GTAATAAATAAAAAGAGTAAGAAAAGA
*
416 GTAAAAAATAATAAA-AGTA
1 GTAATAAATAA-AAAGAGTA
435 GCAAAAGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
27 26 0.65
28 14 0.35
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.18
Consensus pattern (27 bp):
GTAATAAATAAAAAGAGTAAGAAAAGA
Found at i:3157 original size:13 final size:14
Alignment explanation
Indices: 3132--3178 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
3122 TTCAAAAGTT
3132 GTTTTCAACAAAAGA
1 GTTTTCAA-AAAAGA
3147 -TTTTCAAAAAAGA
1 GTTTTCAAAAAAGA
*
3160 GTTTTCAAAAAATA
1 GTTTTCAAAAAAGA
3174 GTTTT
1 GTTTT
3179 GTGTTTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 6 0.20
14 24 0.80
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.36
Consensus pattern (14 bp):
GTTTTCAAAAAAGA
Found at i:3824 original size:16 final size:16
Alignment explanation
Indices: 3798--3847 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
3788 CAACTCAAAG
*
3798 AAGAAAGAAAAAAGAA
1 AAGAAAAAAAAAAGAA
*
3814 GAG-AAAAAAAAAGAAA
1 AAGAAAAAAAAAAG-AA
*
3830 AAGAAAAAGAAAAGAA
1 AAGAAAAAAAAAAGAA
3846 AA
1 AA
3848 ACCATGACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 9 0.32
16 10 0.36
17 9 0.32
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAAAGAA
Found at i:3826 original size:22 final size:23
Alignment explanation
Indices: 3795--3848 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 23
3785 ATTCAACTCA
*
3795 AAGAAGAAAGAAAAA-AGAAGAGAA
1 AAGAA-AAAGAAAAAGA-AAAAGAA
3819 AA-AAAAAGAAAAAGAAAAAGAA
1 AAGAAAAAGAAAAAGAAAAAGAA
3841 AAGAAAAA
1 AAGAAAAA
3849 CCATGACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 17 0.63
23 8 0.30
24 2 0.07
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAAAGAAAAAGAA
Found at i:3845 original size:27 final size:29
Alignment explanation
Indices: 3794--3848 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 29
3784 CATTCAACTC
*
3794 AAAGAAGAAAGAAAAAAGAAGAGAAAAAA
1 AAAGAAGAAAGAAAAAAGAAAAGAAAAAA
3823 AAAGAA-AAAG-AAAAAGAAAAGAAAAA
1 AAAGAAGAAAGAAAAAAGAAAAGAAAAA
3849 CCATGACCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 15 0.60
28 4 0.16
29 6 0.24
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (29 bp):
AAAGAAGAAAGAAAAAAGAAAAGAAAAAA
Found at i:3848 original size:12 final size:11
Alignment explanation
Indices: 3794--3848 Score: 60
Period size: 11 Copynumber: 4.8 Consensus size: 11
3784 CATTCAACTC
3794 AAAGAAGAAAGA
1 AAAGAA-AAAGA
3806 AAA-AAGAAGAGA
1 AAAGAA-AA-AGA
3818 AAA-AAAAAGAA
1 AAAGAAAAAG-A
3829 AAAGAAAAAGA
1 AAAGAAAAAGA
3840 AAAGAAAAA
1 AAAGAAAAA
3849 CCATGACCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
10 2 0.05
11 21 0.52
12 17 0.43
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:6200 original size:26 final size:27
Alignment explanation
Indices: 6130--6202 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 27
6120 AGGGTCATCC
6130 AGGGTTATTTTGGTCATTTTCACATCAT
1 AGGG-TATTTTGGTCATTTTCACATCAT
*
6158 AGGGGCATTTTGGTCATTCTTGCAC-T-A-
1 A-GGGTATTTTGGTCATT-TT-CACATCAT
6185 AGGGTATTTTGGTCATTT
1 AGGGTATTTTGGTCATTT
6203 GCATATTTAG
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
25 1 0.03
26 15 0.38
27 1 0.03
28 14 0.35
29 6 0.15
30 3 0.08
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.44
Consensus pattern (27 bp):
AGGGTATTTTGGTCATTTTCACATCAT
Done.