Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009758.1 Corchorus capsularis cultivar CVL-1 contig09779, 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: 39669
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:1291 original size:35 final size:35
Alignment explanation
Indices: 1241--1404 Score: 233
Period size: 35 Copynumber: 4.7 Consensus size: 35
1231 AGTAATAAGT
* *
1241 AACTTAATTCGGGGTAATTAAGTAATTCAGGAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* *
1276 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1311 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
* *
1346 AACTGTAATTCAGGGTAATTAAGTGAGTT-AATAAGT-
1 AACT-TAATTCAGGGTAATTAAGT-AATTCAGTAA-TC
1382 AACTTAATTCAGGGTAATTAAGT
1 AACTTAATTCAGGGTAATTAAGT
1405 TTAGTAAGAA
Statistics
Matches: 118, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
35 87 0.74
36 27 0.23
37 4 0.03
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (35 bp):
AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
Found at i:1390 original size:71 final size:70
Alignment explanation
Indices: 1233--1404 Score: 283
Period size: 71 Copynumber: 2.4 Consensus size: 70
1223 GGTGAATCAG
*
1233 TAATAAGTAACTTAATTCGGGGTAATTAAGTAATTCAGGAATCAACTTAATTCAGGGTAATTAAG
1 TAATAAGTAACTTAATTCAGGGTAATTAAGTAATTCAGGAATCAACTTAATTCAGGGTAATTAAG
1298 TGAGT
66 TGAGT
* * *
1303 CAGTAA-TCAACTTAATTCAGGGTAATTAAGTAATTCAGTAATCAACTGTAATTCAGGGTAATTA
1 TAATAAGT-AACTTAATTCAGGGTAATTAAGTAATTCAGGAATCAACT-TAATTCAGGGTAATTA
1367 AGTGAGT
64 AGTGAGT
1374 TAATAAGTAACTTAATTCAGGGTAATTAAGT
1 TAATAAGTAACTTAATTCAGGGTAATTAAGT
1405 TTAGTAAGAA
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
69 1 0.01
70 41 0.44
71 50 0.54
72 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (70 bp):
TAATAAGTAACTTAATTCAGGGTAATTAAGTAATTCAGGAATCAACTTAATTCAGGGTAATTAAG
TGAGT
Found at i:5473 original size:16 final size:16
Alignment explanation
Indices: 5443--5476 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5433 ATTTGAAAAA
**
5443 TTGATGATTTCTTGAT
1 TTGATGATTAATTGAT
5459 TTGATGATTAATTGAT
1 TTGATGATTAATTGAT
5475 TT
1 TT
5477 CCAACCTGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.18, T:0.56
Consensus pattern (16 bp):
TTGATGATTAATTGAT
Found at i:5634 original size:2 final size:2
Alignment explanation
Indices: 5627--5651 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5617 ATTGTGTATT
5627 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5652 GATTTATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6437 original size:39 final size:39
Alignment explanation
Indices: 6383--6458 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
6373 CACTTTGCAT
* *
6383 CCTCCTTTTTTATTTTGATCACTTTGCACTGTAATGTAC
1 CCTCCTTTTTTATTTTGATCACTTTACACCGTAATGTAC
6422 CCTCCTTTTTTATTTTGATCACTTTACACCGTAATGT
1 CCTCCTTTTTTATTTTGATCACTTTACACCGTAATGT
6459 TTTATTTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.18, C:0.24, G:0.09, T:0.49
Consensus pattern (39 bp):
CCTCCTTTTTTATTTTGATCACTTTACACCGTAATGTAC
Found at i:13630 original size:49 final size:49
Alignment explanation
Indices: 13532--13630 Score: 153
Period size: 49 Copynumber: 2.0 Consensus size: 49
13522 AGAGTTTATC
* *
13532 AATCCATTGTAATATATCAAAAGTATTTCAATTTATAGGATATATGCAA
1 AATCCATTGTAATATATCAAAAGTATTTCAATTTATAGGATACAAGCAA
** *
13581 AATCCATTGTAATATATTGAAAGTGTTTCAATTTATAGGATACAAGCAA
1 AATCCATTGTAATATATCAAAAGTATTTCAATTTATAGGATACAAGCAA
13630 A
1 A
13631 TACATAGCGC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (49 bp):
AATCCATTGTAATATATCAAAAGTATTTCAATTTATAGGATACAAGCAA
Found at i:17057 original size:230 final size:230
Alignment explanation
Indices: 16654--17110 Score: 851
Period size: 230 Copynumber: 2.0 Consensus size: 230
16644 TGTGTTTTTT
* *
16654 ACTTTGACAATGTGGTTGTAAATTTTAATTGCCACCTTAGCTTCAGATGCAATAATACTGTCTTT
1 ACTTTGACAATGTGGTTGTAAATTTCAATTGCCACCTTACCTTCAGATGCAATAATACTGTCTTT
*
16719 AGTCTCATGCTATTGTACCTTTTTCTGGTATTTGTGAATTAGAATATTGATTGATTTCCTAATTC
66 AGTCTCATGCTACTGTACCTTTTTCTGGTATTTGTGAATTAGAATATTGATTGATTTCCTAATTC
16784 TTCTTCTATGCTTGAATTTCTATCGTTTCTTGTAGTGATAAGTGGTCCAAAAGGACCTACTCCAG
131 TTCTTCTATGCTTGAATTTCTATCGTTTCTTGTAGTGATAAGTGGTCCAAAAGGACCTACTCCAG
16849 ATTCTGAATTTGAGCACTCATCCATCCCTGCACCG
196 ATTCTGAATTTGAGCACTCATCCATCCCTGCACCG
** *
16884 ACTTTGACAATGTGGTTGTAAATTTCAATTGCCGTCTTACCTTCAGATGCAATAATACTGTTTTT
1 ACTTTGACAATGTGGTTGTAAATTTCAATTGCCACCTTACCTTCAGATGCAATAATACTGTCTTT
16949 AGTCTCATGCTACTGTACCTTTTTCTGGTATTTGTGAATTAGAATATTGATTGATTTCCTAATTC
66 AGTCTCATGCTACTGTACCTTTTTCTGGTATTTGTGAATTAGAATATTGATTGATTTCCTAATTC
*
17014 TTCTTCTATGCTTGAATTTCTGTCGTTTCTTGTAGTGATAAGTGGTCCAAAAGGACCTACTCCAG
131 TTCTTCTATGCTTGAATTTCTATCGTTTCTTGTAGTGATAAGTGGTCCAAAAGGACCTACTCCAG
17079 ATTCTGAATTTGAGCACTCATCCATCCCTGCA
196 ATTCTGAATTTGAGCACTCATCCATCCCTGCA
17111 AACAATATTT
Statistics
Matches: 220, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
230 220 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.40
Consensus pattern (230 bp):
ACTTTGACAATGTGGTTGTAAATTTCAATTGCCACCTTACCTTCAGATGCAATAATACTGTCTTT
AGTCTCATGCTACTGTACCTTTTTCTGGTATTTGTGAATTAGAATATTGATTGATTTCCTAATTC
TTCTTCTATGCTTGAATTTCTATCGTTTCTTGTAGTGATAAGTGGTCCAAAAGGACCTACTCCAG
ATTCTGAATTTGAGCACTCATCCATCCCTGCACCG
Found at i:24892 original size:15 final size:16
Alignment explanation
Indices: 24855--24892 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
24845 TTCAAAAAAC
*
24855 TTCCCTTCCCTCTCCT
1 TTCCTTTCCCTCTCCT
24871 TTCCTTTCCCT-TCCT
1 TTCCTTTCCCTCTCCT
24886 TTCCTTT
1 TTCCTTT
24893 AAAAACTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (16 bp):
TTCCTTTCCCTCTCCT
Found at i:25172 original size:21 final size:21
Alignment explanation
Indices: 25148--25188 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
25138 TACGTATTAG
25148 ATTTGTTACTGTACAGATAAA
1 ATTTGTTACTGTACAGATAAA
25169 ATTTGTTACTGTACAGATAA
1 ATTTGTTACTGTACAGATAA
25189 GAATATTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (21 bp):
ATTTGTTACTGTACAGATAAA
Found at i:26132 original size:6 final size:6
Alignment explanation
Indices: 26121--26153 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
26111 TCGCTTATTA
*
26121 CTCGAG CTCGAG CTCGAG CTCTAG CTCG-G CTCG
1 CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG CTCG
26154 TGAAAAATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.12, C:0.36, G:0.30, T:0.21
Consensus pattern (6 bp):
CTCGAG
Found at i:26668 original size:421 final size:421
Alignment explanation
Indices: 25884--26709 Score: 1564
Period size: 421 Copynumber: 2.0 Consensus size: 421
25874 GAGTCGAAGA
25884 GAGCTAGAGAGGTGAGATGAAGTCAACAAACATTTGGGAAATTTGGAGATTTAGGGTTTGGGTGT
1 GAGCTAGAGAGGTGAGATGAAGTCAACAAACATTTGGGAAATTTGGAGATTTAGGGTTTGGGTGT
25949 TATTTATATAGTAATGGTAAATTTGTAATTAATATCAATAATTTAATAAGGTATTATTGTAATTT
66 TATTTATATAGTAATGGTAAATTTGTAATTAATATCAATAATTTAATAAGGTATTATTGTAATTT
*
26014 AAATAATAACATAAATATATATATTATTAAAAATATATAGGTACTCGTTTAGACTCGCGAGCCGC
131 AAATAATAACATAAATATATATATTATTAAAAATATATAGGTACTCATTTAGACTCGCGAGCCGC
*
26079 TCGAGTCAAGTATTTGAAAGCTAAAGCTCGGCTCGCTTATTACTCGAGCTCGAGCTCGAGCTCTA
196 TCGAGTCAAGTATTTGAAAGCTAAAGCTCGGCTCGCTTATTACTCGAACTCGAGCTCGAGCTCTA
* * *
26144 GCTCGGCTCGTGAAAAATCGAGTCGAACTTGAGTATTCTTTGAGCCGAATACGAGTAGTTCATGA
261 GCTCGGCTCGTGAAAAATCGAGTCGAACTTGAGTATTCTTTGAGCCAAACACGAGTAGCTCATGA
* *
26209 GCAGCTCAACTCATTTACAGCCCTAGTAAGAAACTATTTTCATCACTTCGTCCGGTTTATGAGTT
326 GCAGCTCAACTCATTTACAACCCTAGTAAGAAACTATTTTCATCACTTCGTCCGATTTATGAGTT
26274 AAGTGATACATCAAGTATTATTGGGTGTTAT
391 AAGTGATACATCAAGTATTATTGGGTGTTAT
26305 GAGCTAGAGAGGTGAGATGAAGTCAACAAACATTTGGGAAATTTGGAGATTTAGGGTTTGGGTGT
1 GAGCTAGAGAGGTGAGATGAAGTCAACAAACATTTGGGAAATTTGGAGATTTAGGGTTTGGGTGT
*
26370 TATTTATATAGTAATGGTGAATTTGTAATTAATATCAATAATTTAATAAGGTATTATTGTAATTT
66 TATTTATATAGTAATGGTAAATTTGTAATTAATATCAATAATTTAATAAGGTATTATTGTAATTT
26435 AAATAATAACATAAATATATATATTATTAAAAATATATAGGTGA-TCATTTAGACTCGCGAGCCG
131 AAATAATAACATAAATATATATATTATTAAAAATATATAGGT-ACTCATTTAGACTCGCGAGCCG
26499 CTCGAGTCAAGTATTTGAAAGCTAAAGCTCGGCTCGCTTATTACTCGAACTCGAGCTCGAGCTCT
195 CTCGAGTCAAGTATTTGAAAGCTAAAGCTCGGCTCGCTTATTACTCGAACTCGAGCTCGAGCTCT
26564 AGCTCGGCTCGTGAAAAATCGAGTCGAACTTGAGTATTCTTTGAGCCAAACACGAGTAGCTCATG
260 AGCTCGGCTCGTGAAAAATCGAGTCGAACTTGAGTATTCTTTGAGCCAAACACGAGTAGCTCATG
26629 AGCAGCTCAACTCATTTACAACCCTAGTAAGAAACTATTTTCATCACTTCGTCCGATTTATGAGT
325 AGCAGCTCAACTCATTTACAACCCTAGTAAGAAACTATTTTCATCACTTCGTCCGATTTATGAGT
26694 TAAGTGATACATCAAG
390 TAAGTGATACATCAAG
26710 GTTTCAAGGT
Statistics
Matches: 396, Mismatches: 8, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
421 395 1.00
422 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (421 bp):
GAGCTAGAGAGGTGAGATGAAGTCAACAAACATTTGGGAAATTTGGAGATTTAGGGTTTGGGTGT
TATTTATATAGTAATGGTAAATTTGTAATTAATATCAATAATTTAATAAGGTATTATTGTAATTT
AAATAATAACATAAATATATATATTATTAAAAATATATAGGTACTCATTTAGACTCGCGAGCCGC
TCGAGTCAAGTATTTGAAAGCTAAAGCTCGGCTCGCTTATTACTCGAACTCGAGCTCGAGCTCTA
GCTCGGCTCGTGAAAAATCGAGTCGAACTTGAGTATTCTTTGAGCCAAACACGAGTAGCTCATGA
GCAGCTCAACTCATTTACAACCCTAGTAAGAAACTATTTTCATCACTTCGTCCGATTTATGAGTT
AAGTGATACATCAAGTATTATTGGGTGTTAT
Found at i:26821 original size:106 final size:106
Alignment explanation
Indices: 26636--26847 Score: 424
Period size: 106 Copynumber: 2.0 Consensus size: 106
26626 ATGAGCAGCT
26636 CAACTCATTTACAACCCTAGTAAGAAACTATTTTCATCACTTCGTCCGATTTATGAGTTAAGTGA
1 CAACTCATTTACAACCCTAGTAAGAAACTATTTTCATCACTTCGTCCGATTTATGAGTTAAGTGA
26701 TACATCAAGGTTTCAAGGTAAATCACCTATCACTTATATAG
66 TACATCAAGGTTTCAAGGTAAATCACCTATCACTTATATAG
26742 CAACTCATTTACAACCCTAGTAAGAAACTATTTTCATCACTTCGTCCGATTTATGAGTTAAGTGA
1 CAACTCATTTACAACCCTAGTAAGAAACTATTTTCATCACTTCGTCCGATTTATGAGTTAAGTGA
26807 TACATCAAGGTTTCAAGGTAAATCACCTATCACTTATATAG
66 TACATCAAGGTTTCAAGGTAAATCACCTATCACTTATATAG
26848 TTATAATTTC
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (106 bp):
CAACTCATTTACAACCCTAGTAAGAAACTATTTTCATCACTTCGTCCGATTTATGAGTTAAGTGA
TACATCAAGGTTTCAAGGTAAATCACCTATCACTTATATAG
Found at i:33722 original size:24 final size:25
Alignment explanation
Indices: 33674--33728 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
33664 AACCCTAAAT
**
33674 TTCATTTCTAACAACTTCTTCAAAC
1 TTCATTTCTAACAAAATCTTCAAAC
33699 TTCATTTCTAA-AAAATCTTCAAAC
1 TTCATTTCTAACAAAATCTTCAAAC
33723 -TCATTT
1 TTCATTT
33729 TCCTTCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 6 0.21
24 11 0.39
25 11 0.39
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.42
Consensus pattern (25 bp):
TTCATTTCTAACAAAATCTTCAAAC
Found at i:35452 original size:64 final size:64
Alignment explanation
Indices: 35367--35499 Score: 230
Period size: 64 Copynumber: 2.1 Consensus size: 64
35357 CGGTTGCTAG
* * * *
35367 TTAATCCAACAATGGATTTACACAGATGAGTTAGGCATTTTATCGAACACTTGAAAGGCAAGAA
1 TTAAGCCAACAATGAATTTACACAGATGAGTTAAGCATTTTATCAAACACTTGAAAGGCAAGAA
35431 TTAAGCCAACAATGAATTTACACAGATGAGTTAAGCATTTTATCAAACACTTGAAAGGCAAGAA
1 TTAAGCCAACAATGAATTTACACAGATGAGTTAAGCATTTTATCAAACACTTGAAAGGCAAGAA
35495 TTAAG
1 TTAAG
35500 ATAGATATAT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.26
Consensus pattern (64 bp):
TTAAGCCAACAATGAATTTACACAGATGAGTTAAGCATTTTATCAAACACTTGAAAGGCAAGAA
Found at i:39446 original size:20 final size:21
Alignment explanation
Indices: 39421--39461 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
39411 TACTAATTAA
39421 TTATTTGA-ATATTA-ATTTTT
1 TTATTT-ATATATTATATTTTT
39441 TTATTTATATATTATATTTTT
1 TTATTTATATATTATATTTTT
39462 ACTTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.05
20 12 0.63
21 6 0.32
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
TTATTTATATATTATATTTTT
Done.