Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012760.1 Corchorus capsularis cultivar CVL-1 contig12781, 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: 14486
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Found at i:4535 original size:73 final size:71
Alignment explanation
Indices: 4449--4662 Score: 240
Period size: 73 Copynumber: 3.0 Consensus size: 71
4439 AAGAAGACAA
*
4449 ACTA-GCTTAGTTTCAAGGAGACTAGGTAAAA-AGAAGACTGACTTAATTTTCAAGGAAATTAAG
1 ACTAGGCTTAGTTTCAAGGAAACTAGGTAAAAGA-AAGACTGACTTAA-TTTCAAGGAAATTAAG
*
4512 TAAAGATAG
64 TAAA-AAAG
* *
4521 ACTAGGCTTAGTTTCAAGGAAACTAGGTAAAGGAAAGACTGGCTTAATTTCAAGGAAATTAAGTA
1 ACTAGGCTTAGTTTCAAGGAAACTAGGTAAAAGAAAGACTGACTTAATTTCAAGGAAATTAAGTA
4586 AAAAAG
66 AAAAAG
* * * * *
4592 ACT-GGCTTAATTTCAAGAAAGGAAATTAGGT-AAAGAAACGATTGGCTT-AGTTCAAGGAAATT
1 ACTAGGCTTAGTTTC----AAGGAAACTAGGTAAAAGAAA-GACTGACTTAATTTCAAGGAAATT
4654 AAGTAAAAA
61 AAGTAAAAA
4663 GACCGGCTCA
Statistics
Matches: 126, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
70 10 0.08
71 6 0.05
72 24 0.19
73 65 0.52
74 21 0.17
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.25
Consensus pattern (71 bp):
ACTAGGCTTAGTTTCAAGGAAACTAGGTAAAAGAAAGACTGACTTAATTTCAAGGAAATTAAGTA
AAAAAG
Found at i:4587 original size:109 final size:106
Alignment explanation
Indices: 4453--4660 Score: 240
Period size: 109 Copynumber: 1.9 Consensus size: 106
4443 AGACAAACTA
* * *
4453 GCTTAGTTTCAAGGAGACTAGGTAAAAAGAAGACTGACTTAATTTTC-AAGGAAATTAAGTAAAG
1 GCTTAATTTCAAGGAAACTAAGT-AAAA-AAGACTGACTTAA-TTTCAAAGGAAATTAAGTAAAG
* *
4517 ATA-GACTAGGCTTAGTTTCAAGGAAACTAGGTAAAGGAAAGACTG
63 AAACGA-TAGGCTTAG-TTCAAGGAAACTAAGTAAAGGAAAGACTG
* * *
4562 GCTTAATTTCAAGGAAATTAAGTAAAAAAGACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAG
1 GCTTAATTTCAAGGAAACTAAGTAAAAAAGACTGACTTAATTTC---AAAGGAAATTAAGTAAAG
* *
4627 AAACGATTGGCTTAGTTCAAGGAAATTAAGTAAA
63 AAACGATAGGCTTAGTTCAAGGAAACTAAGTAAA
4661 AAGACCGGCT
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
106 4 0.05
107 12 0.14
108 4 0.05
109 36 0.43
110 26 0.31
111 2 0.02
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.25
Consensus pattern (106 bp):
GCTTAATTTCAAGGAAACTAAGTAAAAAAGACTGACTTAATTTCAAAGGAAATTAAGTAAAGAAA
CGATAGGCTTAGTTCAAGGAAACTAAGTAAAGGAAAGACTG
Found at i:4625 original size:38 final size:35
Alignment explanation
Indices: 4453--4660 Score: 204
Period size: 36 Copynumber: 5.7 Consensus size: 35
4443 AGACAAACTA
* * * *
4453 GCTTAGTTTCAAGGAGACTAGGTAAAAAGAAGACTG
1 GCTTAATTTCAAGGAAATTAGGTAAAGA-AAGACTG
* * *
4489 ACTTAATTTTCAAGGAAATTAAGTAAAGATAGACTAG
1 GCTTAA-TTTCAAGGAAATTAGGTAAAGAAAGACT-G
* *
4526 GCTTAGTTTCAAGGAAACTAGGTAAAGGAAAGACTG
1 GCTTAATTTCAAGGAAATTAGGTAAA-GAAAGACTG
*
4562 GCTTAATTTCAAGGAAATTAAGTAAA-AAAGACTG
1 GCTTAATTTCAAGGAAATTAGGTAAAGAAAGACTG
*
4596 GCTTAATTTCAAGAAAGGAAATTAGGTAAAGAAACGATTG
1 GCTTAATTTC----AAGGAAATTAGGTAAAGAAA-GACTG
* *
4636 GCTT-AGTTCAAGGAAATTAAGTAAA
1 GCTTAATTTCAAGGAAATTAGGTAAA
4661 AAGACCGGCT
Statistics
Matches: 144, Mismatches: 19, Indels: 19
0.79 0.10 0.10
Matches are distributed among these distances:
34 18 0.12
35 15 0.10
36 51 0.35
37 30 0.21
38 15 0.10
39 7 0.05
40 8 0.06
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.25
Consensus pattern (35 bp):
GCTTAATTTCAAGGAAATTAGGTAAAGAAAGACTG
Found at i:4822 original size:36 final size:36
Alignment explanation
Indices: 4724--4828 Score: 138
Period size: 36 Copynumber: 2.9 Consensus size: 36
4714 ATTTCAAGGA
* *
4724 AAGAGATTACGTAAACATCAGCACAGACTTAATTTCAC
1 AAGA-ATTAAGTAAA-ATCAGCAAAGACTTAATTTCAC
* *
4762 AAGAATTAAGTAAAATTAGTAAAGACTTAATTTCAC
1 AAGAATTAAGTAAAATCAGCAAAGACTTAATTTCAC
* *
4798 AAGAATTAAGTAAAGTCAGCAAAGATTTAAT
1 AAGAATTAAGTAAAATCAGCAAAGACTTAAT
4829 CCATAGTTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
36 46 0.78
37 9 0.15
38 4 0.07
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (36 bp):
AAGAATTAAGTAAAATCAGCAAAGACTTAATTTCAC
Found at i:4904 original size:11 final size:11
Alignment explanation
Indices: 4888--4940 Score: 83
Period size: 11 Copynumber: 5.0 Consensus size: 11
4878 TAGGCAAAAC
4888 AAAGAAGACTG
1 AAAGAAGACTG
4899 AAAGAAGACTG
1 AAAGAAGACTG
4910 -AA-AAGACTG
1 AAAGAAGACTG
*
4919 AAAGAAGACTA
1 AAAGAAGACTG
4930 AAAGAAGACTG
1 AAAGAAGACTG
4941 GCTTAATTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
9 7 0.18
10 4 0.11
11 27 0.71
ACGTcount: A:0.57, C:0.09, G:0.25, T:0.09
Consensus pattern (11 bp):
AAAGAAGACTG
Found at i:4917 original size:20 final size:19
Alignment explanation
Indices: 4892--4934 Score: 77
Period size: 20 Copynumber: 2.2 Consensus size: 19
4882 CAAAACAAAG
4892 AAGACTGAAAGAAGACTGAA
1 AAGACTGAAAGAAGACT-AA
4912 AAGACTGAAAGAAGACTAA
1 AAGACTGAAAGAAGACTAA
4931 AAGA
1 AAGA
4935 AGACTGGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.58, C:0.09, G:0.23, T:0.09
Consensus pattern (19 bp):
AAGACTGAAAGAAGACTAA
Found at i:4975 original size:36 final size:36
Alignment explanation
Indices: 4934--5794 Score: 539
Period size: 36 Copynumber: 23.7 Consensus size: 36
4924 AGACTAAAAG
**
4934 AAGACTGGCTTAATTTCAAGGAAATTAATTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
4970 AAGACTGGCTTAGTTTCAAGAAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * * * *
5006 AAGACTGACTCAGTTTCAAGGAAACTACGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
5042 TAGACTGGCTTGATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
5078 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
*
5114 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAA-CA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
5149 TAGACTGGTTTAATTTCAAGGAAATTAGGTAAAGGA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
5185 AAGATTGGCTTAATTTCAAGGAAATTAAGT--A-AA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * * * * * *
5218 AAGACCGGCTCAGTTTTAGGAAAGGAAATTAGTTAAGGAT
1 AAGACTGGCTTA-ATTT---CAAGGAAATTAGGTAAAGAA
* * *
5258 AAGCACAGACTTAATTTCAAGGAAAGAAATTAGGTAAAGAT
1 AAG-ACTGGCTTAATTTCAA-G---GAAATTAGGTAAAGAA
* * * * *
5299 CAGCACAGACTTGATTTCAAGGAAAGAAATTAGGTAAAGAT
1 AAG-ACTGGCTTAATTTCAA-G---GAAATTAGGTAAAGAA
* * * * * * *
5340 CAGCACAGACTTGATTTCACAAG-AATTAAGTAAA-AT
1 AAG-ACTGGCTTAATTTCA-AGGAAATTAGGTAAAGAA
* ** * * *
5376 TAGCAAAGACTTAATTTCACAAG-AATTAAGTAAAGTCAGCA
1 AAG-ACTGGCTTAATTTCA-AGGAAATTAGGTAAAG--A--A
* * *
5417 AAGA-T---TTAA-TCCATA-GATGATTAAGT-AAGATCA
1 AAGACTGGCTTAATTTCA-AGGA-AATTAGGTAAAGA--A
* *
5450 GACAGA-GGGCTTAATTTCAAGGAAATTAGGCAAA-ACA
1 -A-AGACTGGCTTAATTTCAAGGAAATTAGGTAAAGA-A
* * * ** *
5487 AAGA-AGACTGAA--AGAAGACTGAAA--AGACTGAAAG--
1 AAGACTGGCTTAATTTCAAG---GAAATTAG-GT-AAAGAA
* *
5521 AAGACTGGCTTAATTTCAAGGAAGTTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
5557 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
5593 AAGACTGGCTCAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
5629 TAGACTGGCTTGATTTCAAGGAAATTAAGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
5665 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
*
5701 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGGA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* *
5737 AAGACTGGCTTCATTTCAAGGAAATTAAGTAAA-AA
1 AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
* * *
5772 GACACAGGCTTAATTTC-AGGAAA
1 AAGACTGGCTTAATTTCAAGGAAA
5795 GGAAATTAAG
Statistics
Matches: 675, Mismatches: 108, Indels: 86
0.78 0.12 0.10
Matches are distributed among these distances:
33 16 0.02
34 25 0.04
35 70 0.10
36 426 0.63
37 28 0.04
38 13 0.02
39 8 0.01
40 8 0.01
41 80 0.12
42 1 0.00
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (36 bp):
AAGACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA
Found at i:5287 original size:41 final size:41
Alignment explanation
Indices: 5235--5358 Score: 203
Period size: 41 Copynumber: 3.0 Consensus size: 41
5225 GCTCAGTTTT
* * * *
5235 AGGAAAGGAAATTAGTTAAGGATAAGCACAGACTTAATTTCA
1 AGGAAA-GAAATTAGGTAAAGATCAGCACAGACTTGATTTCA
5277 AGGAAAGAAATTAGGTAAAGATCAGCACAGACTTGATTTCA
1 AGGAAAGAAATTAGGTAAAGATCAGCACAGACTTGATTTCA
5318 AGGAAAGAAATTAGGTAAAGATCAGCACAGACTTGATTTCA
1 AGGAAAGAAATTAGGTAAAGATCAGCACAGACTTGATTTCA
5359 CAAGAATTAA
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
41 72 0.92
42 6 0.08
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (41 bp):
AGGAAAGAAATTAGGTAAAGATCAGCACAGACTTGATTTCA
Found at i:5502 original size:11 final size:11
Alignment explanation
Indices: 5486--5527 Score: 70
Period size: 11 Copynumber: 4.0 Consensus size: 11
5476 TAGGCAAAAC
5486 AAAGAAGACTG
1 AAAGAAGACTG
5497 AAAGAAGACTG
1 AAAGAAGACTG
5508 -AA-AAGACTG
1 AAAGAAGACTG
5517 AAAGAAGACTG
1 AAAGAAGACTG
5528 GCTTAATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.24
10 4 0.14
11 18 0.62
ACGTcount: A:0.55, C:0.10, G:0.26, T:0.10
Consensus pattern (11 bp):
AAAGAAGACTG
Found at i:5515 original size:20 final size:20
Alignment explanation
Indices: 5490--5527 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5480 CAAAACAAAG
5490 AAGACTGAAAGAAGACTGAA
1 AAGACTGAAAGAAGACTGAA
5510 AAGACTGAAAGAAGACTG
1 AAGACTGAAAGAAGACTG
5528 GCTTAATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.11, G:0.26, T:0.11
Consensus pattern (20 bp):
AAGACTGAAAGAAGACTGAA
Found at i:5835 original size:32 final size:32
Alignment explanation
Indices: 5798--5921 Score: 162
Period size: 32 Copynumber: 3.8 Consensus size: 32
5788 CAGGAAAGGA
5798 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
1 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
*
5830 AATTAAGTGAAGTCAATAAA-AGGCTTAATTCAGGGT
1 AATTAAGT-AA---AATAAAGA-ACTTAATTCAGGGT
* *
5866 AATTAAGTAGAATAAAGAACTTAATTCAAGGT
1 AATTAAGTAAAATAAAGAACTTAATTCAGGGT
5898 AATTAAGTAAAA-AAAGAACTTAAT
1 AATTAAGTAAAATAAAGAACTTAAT
5922 CTAAAAAGAG
Statistics
Matches: 81, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
31 12 0.15
32 37 0.46
33 3 0.04
35 2 0.02
36 27 0.33
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.27
Consensus pattern (32 bp):
AATTAAGTAAAATAAAGAACTTAATTCAGGGT
Found at i:14249 original size:13 final size:13
Alignment explanation
Indices: 14203--14250 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
14193 TATTATTTTT
14203 TCTCTTTTCTTAC
1 TCTCTTTTCTTAC
* *
14216 TCT-TTTTACTAAT
1 TCTCTTTT-CTTAC
14229 TACTCTTTTCTTAC
1 T-CTCTTTTCTTAC
14243 TCTCTTTT
1 TCTCTTTT
14251 ATTTATTACC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
12 4 0.14
13 14 0.50
14 6 0.21
15 4 0.14
ACGTcount: A:0.12, C:0.25, G:0.00, T:0.62
Consensus pattern (13 bp):
TCTCTTTTCTTAC
Found at i:14265 original size:29 final size:28
Alignment explanation
Indices: 14206--14278 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 28
14196 TATTTTTTCT
*
14206 CTTTTCTTACTCT-TTTTACTAATTACT
1 CTTTTCTTACTCTCTTTTACTAATTACA
* *
14233 CTTTTCTTACTCTCTTTTATTTATTACCA
1 CTTTTCTTACTCTCTTTTACTAATTA-CA
14262 C-TTT-TTACTCTTCTTTT
1 CTTTTCTTACTC-TCTTTT
14279 TTCTTATACT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 19 0.47
28 19 0.47
29 2 0.05
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (28 bp):
CTTTTCTTACTCTCTTTTACTAATTACA
Found at i:14363 original size:21 final size:21
Alignment explanation
Indices: 14324--14414 Score: 112
Period size: 21 Copynumber: 4.3 Consensus size: 21
14314 CTGATCACCC
*
14324 TTTTACTCTTTACTGATTATTA
1 TTTTACTC-TTACTGATTACTA
* *
14346 TTTTACTCTTACTAATTACCA
1 TTTTACTCTTACTGATTACTA
*
14367 TTTTGCTCTTACTGATTACTA
1 TTTTACTCTTACTGATTACTA
* *
14388 TTTGACTCTTACTGATTAC-C
1 TTTTACTCTTACTGATTACTA
14408 TTTTACT
1 TTTTACT
14415 GATTACTATT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 6 0.10
21 45 0.76
22 8 0.14
ACGTcount: A:0.22, C:0.20, G:0.05, T:0.53
Consensus pattern (21 bp):
TTTTACTCTTACTGATTACTA
Found at i:14384 original size:42 final size:42
Alignment explanation
Indices: 14322--14473 Score: 136
Period size: 42 Copynumber: 3.6 Consensus size: 42
14312 TACTGATCAC
* *
14322 CCTTTTACTCTTTACTGATTATTATTTTACTCTTACTAATTA
1 CCTTTTACTCTTTACTGATTACTATTTGACTCTTACTAATTA
* *
14364 CCATTTTGCTC-TTACTGATTACTATTTGACTCTTACTGATTA
1 CC-TTTTACTCTTTACTGATTACTATTTGACTCTTACTAATTA
** * *
14406 CCTTTTACTGATTACT-ATTTTACTCTTTTGA--ATT--TAATTA
1 CCTTTTACTCTTTACTGA--TTACT-ATTTGACTCTTACTAATTA
*
14446 CCTTCTTACTTTTTACTGATTACTATTT
1 CCTT-TTACTCTTTACTGATTACTATTT
14474 TTGCTTCTCA
Statistics
Matches: 91, Mismatches: 12, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
39 3 0.03
40 14 0.15
41 17 0.19
42 40 0.44
43 12 0.13
44 5 0.05
ACGTcount: A:0.22, C:0.19, G:0.05, T:0.53
Consensus pattern (42 bp):
CCTTTTACTCTTTACTGATTACTATTTGACTCTTACTAATTA
Found at i:14421 original size:21 final size:20
Alignment explanation
Indices: 14311--14414 Score: 102
Period size: 21 Copynumber: 5.0 Consensus size: 20
14301 ACTCTTTGAA
*
14311 TTACTGATCACCCTTTTACTC
1 TTACTGATTA-CCTTTTACTC
**
14332 TTTACTGATTATTATTTTACTC
1 -TTACTGATTA-CCTTTTACTC
* *
14354 TTACTAATTACCATTTTGCTC
1 TTACTGATTACC-TTTTACTC
14375 TTACTGATTA-CTATTTGACTC
1 TTACTGATTACCT-TTT-ACTC
14396 TTACTGATTACCTTTTACT
1 TTACTGATTACCTTTTACT
14415 GATTACTATT
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
19 1 0.01
20 7 0.10
21 41 0.60
22 19 0.28
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (20 bp):
TTACTGATTACCTTTTACTC
Done.