Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008117.1 Corchorus capsularis cultivar CVL-1 contig08138, 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: 30539
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:4509 original size:30 final size:30
Alignment explanation
Indices: 4475--4532 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4465 AGCTCCACCG
* *
4475 CCGAAGCCAGCACCTCCTCCTCCACCAACA
1 CCGAAGCCACCACCTCCACCTCCACCAACA
*
4505 CCGAAGCCACCACCTCCACCTCCGCCAA
1 CCGAAGCCACCACCTCCACCTCCACCAA
4533 ATCCTCCTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.26, C:0.55, G:0.10, T:0.09
Consensus pattern (30 bp):
CCGAAGCCACCACCTCCACCTCCACCAACA
Found at i:4669 original size:30 final size:30
Alignment explanation
Indices: 4635--4716 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
4625 CCAACTCCAC
* * *
4635 CACCACCACCAAATCCTCCTCCACCCCCTG
1 CACCACCACCAAAGCCTCCACCACCACCTG
* *
4665 CACCACCTCCAAGGCCTCCACCACCACCTG
1 CACCACCACCAAAGCCTCCACCACCACCTG
* * *
4695 CACCACCCCCGAAGCCACCACC
1 CACCACCACCAAAGCCTCCACC
4717 GGCACCACCG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.24, C:0.60, G:0.07, T:0.09
Consensus pattern (30 bp):
CACCACCACCAAAGCCTCCACCACCACCTG
Found at i:4675 original size:42 final size:42
Alignment explanation
Indices: 4583--4675 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
4573 TCCACCTTTT
* * * ** *
4583 CCAAATCCACCACCAGCTCCAAATCCTCCTCCACTTCCTCCT
1 CCAACTCCACCACCACCACCAAATCCTCCTCCACCCCCTCCA
*
4625 CCAACTCCACCACCACCACCAAATCCTCCTCCACCCCCTGCA
1 CCAACTCCACCACCACCACCAAATCCTCCTCCACCCCCTCCA
*
4667 CCACCTCCA
1 CCAACTCCA
4676 AGGCCTCCAC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.25, C:0.57, G:0.02, T:0.16
Consensus pattern (42 bp):
CCAACTCCACCACCACCACCAAATCCTCCTCCACCCCCTCCA
Found at i:4700 original size:12 final size:12
Alignment explanation
Indices: 4683--4759 Score: 50
Period size: 12 Copynumber: 6.4 Consensus size: 12
4673 CCAAGGCCTC
4683 CACCACCACCTG
1 CACCACCACCTG
*
4695 CACCACC-CCCG
1 CACCACCACCTG
* *
4706 AAGCCACCACCGG
1 CA-CCACCACCTG
* *
4719 CACCACCGCCAG
1 CACCACCACCTG
*
4731 CACCACCTCCT-
1 CACCACCACCTG
* *
4742 AAGCCACCACCTC
1 CA-CCACCACCTG
4755 CACCA
1 CACCA
4760 AGACCCCCTC
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
11 5 0.10
12 40 0.80
13 5 0.10
ACGTcount: A:0.26, C:0.58, G:0.10, T:0.05
Consensus pattern (12 bp):
CACCACCACCTG
Found at i:4736 original size:24 final size:23
Alignment explanation
Indices: 4683--4737 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
4673 CCAAGGCCTC
* *
4683 CACCACCACCTGCACCACCCCCG
1 CACCACCACCGGCACCACCCCAG
*
4706 AAGCCACCACCGGCACCACCGCCAG
1 CA-CCACCACCGGCACCACC-CCAG
4731 CACCACC
1 CACCACC
4738 TCCTAAGCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 1 0.04
24 21 0.81
25 4 0.15
ACGTcount: A:0.25, C:0.60, G:0.13, T:0.02
Consensus pattern (23 bp):
CACCACCACCGGCACCACCCCAG
Found at i:4759 original size:36 final size:36
Alignment explanation
Indices: 4679--4759 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
4669 ACCTCCAAGG
*
4679 CCTCCACCACCACCTGCACCACCCCCGAAGCCACCA
1 CCTCCACCACCACCAGCACCACCCCCGAAGCCACCA
** * * *
4715 CCGGCACCACCGCCAGCACCACCTCCTAAGCCACCA
1 CCTCCACCACCACCAGCACCACCCCCGAAGCCACCA
4751 CCTCCACCA
1 CCTCCACCA
4760 AGACCCCCTC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.25, C:0.59, G:0.10, T:0.06
Consensus pattern (36 bp):
CCTCCACCACCACCAGCACCACCCCCGAAGCCACCA
Found at i:4812 original size:24 final size:24
Alignment explanation
Indices: 4785--4831 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4775 CCTGCTCCCC
*
4785 CACCAA-GTCCACCTCCTCCACCAG
1 CACCAATG-CCACCACCTCCACCAG
*
4809 CACCAATGCCGCCACCTCCACCA
1 CACCAATGCCACCACCTCCACCA
4832 AGTCCACCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.26, C:0.55, G:0.09, T:0.11
Consensus pattern (24 bp):
CACCAATGCCACCACCTCCACCAG
Found at i:4823 original size:18 final size:18
Alignment explanation
Indices: 4802--4849 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
4792 TCCACCTCCT
*
4802 CCACCAGCACCAA-TGCCG
1 CCACCAGCACCAAGT-CCA
**
4820 CCACCTCCACCAAGTCCA
1 CCACCAGCACCAAGTCCA
4838 CCACCAGCACCA
1 CCACCAGCACCA
4850 CCACCTAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.29, C:0.54, G:0.10, T:0.06
Consensus pattern (18 bp):
CCACCAGCACCAAGTCCA
Found at i:4910 original size:42 final size:42
Alignment explanation
Indices: 4845--4968 Score: 185
Period size: 42 Copynumber: 3.0 Consensus size: 42
4835 CCACCACCAG
* * *
4845 CACCACCACCTAAACCCCCTCCTGCACCTCCACCAAGTCCGC
1 CACCACCTCCTAATCCACCTCCTGCACCTCCACCAAGTCCGC
* *
4887 CACCGCCTCCTAATCCACCTCCTGCACCTCCACCAAGTCCTC
1 CACCACCTCCTAATCCACCTCCTGCACCTCCACCAAGTCCGC
* *
4929 CACCACCTCCCAATCCACCTCCTGCACCTCCGCCAAGTCC
1 CACCACCTCCTAATCCACCTCCTGCACCTCCACCAAGTCC
4969 ATGGCCACCT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.21, C:0.56, G:0.07, T:0.15
Consensus pattern (42 bp):
CACCACCTCCTAATCCACCTCCTGCACCTCCACCAAGTCCGC
Found at i:5055 original size:72 final size:72
Alignment explanation
Indices: 4973--5154 Score: 206
Period size: 72 Copynumber: 2.5 Consensus size: 72
4963 AAGTCCATGG
*
4973 CCACCTCCAAGTCCTCCACCACCACCTAATCCACCTCCTTTGCCAAGTCCATGACCACCACCTAA
1 CCACCACCAAGTCCTCCACCACCACCTAATCCACCTCCTTTGCCAAGTCCATGACCACCACC-AA
5038 -TCCACCT
65 GTCCACCT
**** * * * * **
5045 CCTTTGCCAAGTCCAT-GACCACCCCCTAAACCACCTCCTTTGCCAAGTCCATGGCCATGACCAA
1 CCACCACCAAGTCC-TCCACCACCACCTAATCCACCTCCTTTGCCAAGTCCATGACCACCACCAA
*
5109 GTCCTCCT
65 GTCCACCT
* *
5117 CCACCACCAAGGCCGCCACCACCACCTAATCCACCTCC
1 CCACCACCAAGTCCTCCACCACCACCTAATCCACCTCC
5155 CGCTCCACCA
Statistics
Matches: 87, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
71 2 0.02
72 84 0.97
73 1 0.01
ACGTcount: A:0.24, C:0.49, G:0.09, T:0.18
Consensus pattern (72 bp):
CCACCACCAAGTCCTCCACCACCACCTAATCCACCTCCTTTGCCAAGTCCATGACCACCACCAAG
TCCACCT
Found at i:5118 original size:36 final size:36
Alignment explanation
Indices: 4990--5097 Score: 198
Period size: 36 Copynumber: 3.0 Consensus size: 36
4980 CAAGTCCTCC
4990 ACCACCACCTAATCCACCTCCTTTGCCAAGTCCATG
1 ACCACCACCTAATCCACCTCCTTTGCCAAGTCCATG
5026 ACCACCACCTAATCCACCTCCTTTGCCAAGTCCATG
1 ACCACCACCTAATCCACCTCCTTTGCCAAGTCCATG
* *
5062 ACCACCCCCTAAACCACCTCCTTTGCCAAGTCCATG
1 ACCACCACCTAATCCACCTCCTTTGCCAAGTCCATG
5098 GCCATGACCA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.25, C:0.45, G:0.08, T:0.21
Consensus pattern (36 bp):
ACCACCACCTAATCCACCTCCTTTGCCAAGTCCATG
Found at i:5167 original size:24 final size:24
Alignment explanation
Indices: 5133--5190 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
5123 CCAAGGCCGC
*
5133 CACCACCACCTAATCCACCTCCCG
1 CACCACCACCTAAACCACCTCCCG
* * *
5157 CTCCACCACCTAAACCTCCTCCTG
1 CACCACCACCTAAACCACCTCCCG
5181 CACCACCACC
1 CACCACCACC
5191 GAGACCTCCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.24, C:0.59, G:0.03, T:0.14
Consensus pattern (24 bp):
CACCACCACCTAAACCACCTCCCG
Found at i:5197 original size:24 final size:23
Alignment explanation
Indices: 5133--5199 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 23
5123 CCAAGGCCGC
*
5133 CACCACCACCTAATCCACCTCCCG
1 CACCACCACCTAA-CCTCCTCCCG
* *
5157 CTCCACCACCTAAACCTCCTCCTG
1 CACCACCACCT-AACCTCCTCCCG
*
5181 CACCACCACCGAGACCTCC
1 CACCACCACCTA-ACCTCC
5200 ACCACCACCT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 33 0.92
25 2 0.06
ACGTcount: A:0.24, C:0.57, G:0.06, T:0.13
Consensus pattern (23 bp):
CACCACCACCTAACCTCCTCCCG
Found at i:5202 original size:18 final size:18
Alignment explanation
Indices: 5181--5220 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5171 CCTCCTCCTG
5181 CACCACCACCGAGACCTC
1 CACCACCACCGAGACCTC
* *
5199 CACCACCACCTAGGCCTC
1 CACCACCACCGAGACCTC
5217 CACC
1 CACC
5221 TCCGCCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.57, G:0.10, T:0.07
Consensus pattern (18 bp):
CACCACCACCGAGACCTC
Found at i:5209 original size:12 final size:12
Alignment explanation
Indices: 5194--5323 Score: 55
Period size: 12 Copynumber: 10.8 Consensus size: 12
5184 CACCACCGAG
5194 ACCTCCACCACC
1 ACCTCCACCACC
*** *
5206 ACCTAGGCCTCC
1 ACCTCCACCACC
* *
5218 ACCTCCGCCA-A
1 ACCTCCACCACC
*
5229 ATCCTCCACCCCC
1 A-CCTCCACCACC
* * **
5242 ACCGCCCCCAAG
1 ACCTCCACCACC
* *
5254 ACCACCTCCACC
1 ACCTCCACCACC
**
5266 ACCTAAACCACC
1 ACCTCCACCACC
* *
5278 ACCACCACCAGC
1 ACCTCCACCACC
**
5290 ACCTCCACCAAA
1 ACCTCCACCACC
*
5302 ACCTCCACCAGC
1 ACCTCCACCACC
*
5314 ACCACCACCA
1 ACCTCCACCA
5324 ATGCCTCCTC
Statistics
Matches: 82, Mismatches: 34, Indels: 4
0.68 0.28 0.03
Matches are distributed among these distances:
11 1 0.01
12 80 0.98
13 1 0.01
ACGTcount: A:0.28, C:0.58, G:0.05, T:0.08
Consensus pattern (12 bp):
ACCTCCACCACC
Found at i:5281 original size:6 final size:6
Alignment explanation
Indices: 5254--5323 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 6
5244 CGCCCCCAAG
* * * * **
5254 ACCACC TCCACC ACCTA-A ACCACC ACCACC ACCAGC ACCTCC ACCAAA
1 ACCACC ACCACC ACC-ACC ACCACC ACCACC ACCACC ACCACC ACCACC
* *
5302 ACCTCC ACCAGC ACCACC ACCA
1 ACCACC ACCACC ACCACC ACCA
5324 ATGCCTCCTC
Statistics
Matches: 46, Mismatches: 16, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
5 1 0.02
6 44 0.96
7 1 0.02
ACGTcount: A:0.34, C:0.57, G:0.03, T:0.06
Consensus pattern (6 bp):
ACCACC
Found at i:5281 original size:24 final size:22
Alignment explanation
Indices: 5254--5323 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 22
5244 CGCCCCCAAG
5254 ACCACCTCCACCACCTAAACCACC
1 ACCACCTCCACCACCT--ACCACC
* *
5278 ACCACCACCAGCACCT-CCACC
1 ACCACCTCCACCACCTACCACC
** *
5299 AAAACCTCCACCAGC-ACCACC
1 ACCACCTCCACCACCTACCACC
5320 ACCA
1 ACCA
5324 ATGCCTCCTC
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
21 22 0.61
24 14 0.39
ACGTcount: A:0.34, C:0.57, G:0.03, T:0.06
Consensus pattern (22 bp):
ACCACCTCCACCACCTACCACC
Found at i:5317 original size:39 final size:39
Alignment explanation
Indices: 5216--5349 Score: 111
Period size: 36 Copynumber: 3.6 Consensus size: 39
5206 ACCTAGGCCT
* * ** * *
5216 CCACCTCCGCCAAATCCTCCACCCCCACCGCCCCCAA-G
1 CCACCTCCACCAAAACCTCCACCAGCACCACCACCAATG
** *
5254 ACCACCTCCACC---ACCTAAACCACCACCACCACC-A-G
1 -CCACCTCCACCAAAACCTCCACCAGCACCACCACCAATG
5289 -CACCTCCACCAAAACCTCCACCAGCACCACCACCAATG
1 CCACCTCCACCAAAACCTCCACCAGCACCACCACCAATG
* *
5327 CCTCCTCCACCTAAACCTCCACC
1 CCACCTCCACCAAAACCTCCACC
5350 CCCTCCAAAG
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
33 10 0.13
35 2 0.03
36 33 0.43
37 1 0.01
38 1 0.01
39 30 0.39
ACGTcount: A:0.28, C:0.58, G:0.04, T:0.09
Consensus pattern (39 bp):
CCACCTCCACCAAAACCTCCACCAGCACCACCACCAATG
Found at i:11325 original size:5 final size:5
Alignment explanation
Indices: 11309--11352 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
11299 TGTAAAGACA
* *
11309 AAAAT AAGAT AAAAT AAAAT AAAAC AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
11353 AGTTGTCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:23873 original size:13 final size:13
Alignment explanation
Indices: 23855--23886 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
23845 GATATAAATT
23855 TATTTAAATATTA
1 TATTTAAATATTA
23868 TATTTAAATATTA
1 TATTTAAATATTA
23881 TATTTA
1 TATTTA
23887 TCTTATAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTAAATATTA
Found at i:24294 original size:55 final size:55
Alignment explanation
Indices: 24221--24340 Score: 204
Period size: 55 Copynumber: 2.2 Consensus size: 55
24211 AACTGAAACC
* * *
24221 GAACCGGAACAAGAACATCTACCATAAGGTTAAGGTTTCAATTCTAAAAACTTTA
1 GAACCGAAACAAGAACATCTACCAGAAGATTAAGGTTTCAATTCTAAAAACTTTA
*
24276 GAACCGAAACAAGAACATCTACTAGAAGATTAAGGTTTCAATTCTAAAAACTTTA
1 GAACCGAAACAAGAACATCTACCAGAAGATTAAGGTTTCAATTCTAAAAACTTTA
24331 GAACCGAAAC
1 GAACCGAAAC
24341 TAAACCATGA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.23
Consensus pattern (55 bp):
GAACCGAAACAAGAACATCTACCAGAAGATTAAGGTTTCAATTCTAAAAACTTTA
Found at i:24726 original size:35 final size:35
Alignment explanation
Indices: 24686--24754 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
24676 TTGAGTGGCA
24686 TTGAGTGGCATAAACTACCTTAACTCAGATATTCG
1 TTGAGTGGCATAAACTACCTTAACTCAGATATTCG
*
24721 TTGAGTGGCATAAACTACGTTAACTCAGATATTC
1 TTGAGTGGCATAAACTACCTTAACTCAGATATTC
24755 TAATAATATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (35 bp):
TTGAGTGGCATAAACTACCTTAACTCAGATATTCG
Found at i:25526 original size:21 final size:20
Alignment explanation
Indices: 25484--25527 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
25474 TGGTAAGACT
* *
25484 TTTAAGATGAATTGTTGAGG
1 TTTAAGATAAATCGTTGAGG
*
25504 TTTAAGACTAAATCGTTGTGG
1 TTTAAGA-TAAATCGTTGAGG
25525 TTT
1 TTT
25528 TGGTAATTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.43
Consensus pattern (20 bp):
TTTAAGATAAATCGTTGAGG
Done.