Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010537.1 Corchorus capsularis cultivar CVL-1 contig10558, 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: 81176
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3941 original size:13 final size:13
Alignment explanation
Indices: 3910--3942 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3900 ATGAAAAAAC
3910 AAATA-ATTACAA
1 AAATAGATTACAA
3922 AAA-AGATTACAA
1 AAATAGATTACAA
3934 AAATAGATT
1 AAATAGATT
3943 TCTCAGTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.05
12 13 0.68
13 5 0.26
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (13 bp):
AAATAGATTACAA
Found at i:4124 original size:12 final size:12
Alignment explanation
Indices: 4085--4128 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
4075 TAATCCGACC
*
4085 TTTTT-TTGCCA
1 TTTTTCTTGGCA
* *
4096 TTTTCCTTCGCA
1 TTTTTCTTGGCA
4108 TTTTTCTTGGCA
1 TTTTTCTTGGCA
4120 TTTTTCTTG
1 TTTTTCTTG
4129 TGTTTCTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 4 0.15
12 23 0.85
ACGTcount: A:0.07, C:0.20, G:0.11, T:0.61
Consensus pattern (12 bp):
TTTTTCTTGGCA
Found at i:4210 original size:22 final size:22
Alignment explanation
Indices: 4180--4283 Score: 82
Period size: 22 Copynumber: 4.9 Consensus size: 22
4170 GAAGAGCATA
4180 AACAGAGGAAATCAAGCAAAAAG
1 AACAGAGGAAATCAAG-AAAAAG
4203 AA-AGAGGAAAT-AAG-AAAAG
1 AACAGAGGAAATCAAGAAAAAG
*
4222 AACACA-G--ATCAAGAAGAGCATA-
1 AACAGAGGAAATCAAGAA-A--A-AG
4244 AACAGAGGAAATCAAGCAAAAAG
1 AACAGAGGAAATCAAG-AAAAAG
4267 AA-AGAGGAAAT-AAGAAA
1 AACAGAGGAAATCAAGAAA
4284 CAAACCTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 27
0.70 0.02 0.28
Matches are distributed among these distances:
17 2 0.03
18 3 0.04
19 9 0.13
20 6 0.09
21 6 0.09
22 25 0.37
23 7 0.10
25 7 0.10
26 2 0.03
ACGTcount: A:0.62, C:0.10, G:0.22, T:0.06
Consensus pattern (22 bp):
AACAGAGGAAATCAAGAAAAAG
Found at i:4254 original size:64 final size:64
Alignment explanation
Indices: 4153--4283 Score: 262
Period size: 64 Copynumber: 2.0 Consensus size: 64
4143 CCTGCTTAAA
4153 AAAAGAACACAGATCAAGAAGAGCATAAACAGAGGAAATCAAGCAAAAAGAAAGAGGAAATAAG
1 AAAAGAACACAGATCAAGAAGAGCATAAACAGAGGAAATCAAGCAAAAAGAAAGAGGAAATAAG
4217 AAAAGAACACAGATCAAGAAGAGCATAAACAGAGGAAATCAAGCAAAAAGAAAGAGGAAATAAG
1 AAAAGAACACAGATCAAGAAGAGCATAAACAGAGGAAATCAAGCAAAAAGAAAGAGGAAATAAG
4281 AAA
1 AAA
4284 CAAACCTTTC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.62, C:0.11, G:0.21, T:0.06
Consensus pattern (64 bp):
AAAAGAACACAGATCAAGAAGAGCATAAACAGAGGAAATCAAGCAAAAAGAAAGAGGAAATAAG
Found at i:6611 original size:41 final size:42
Alignment explanation
Indices: 6554--6637 Score: 161
Period size: 41 Copynumber: 2.0 Consensus size: 42
6544 CGTGCAGCTG
6554 TTTTATTTTATAAATTCTTTTAAG-AAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
6595 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
1 TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
6637 T
1 T
6638 GAAATTTTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 24 0.57
42 18 0.43
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (42 bp):
TTTTATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAA
Found at i:6645 original size:42 final size:41
Alignment explanation
Indices: 6558--6645 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 41
6548 CAGCTGTTTT
***
6558 ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATTTT
1 ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATGAA
6599 ATTTTATAAATTCTTTTAAGAAAAATTCAGTTAAGAAATGAA
1 ATTTTATAAATTCTTTTAAG-AAAATTCAGTTAAGAAATGAA
6641 ATTTT
1 ATTTT
6646 GTTGTGAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
41 20 0.47
42 23 0.53
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (41 bp):
ATTTTATAAATTCTTTTAAGAAAATTCAGTTAAGAAATGAA
Found at i:13917 original size:25 final size:24
Alignment explanation
Indices: 13881--13947 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 24
13871 TCTTAACCTT
*
13881 CAAATCCT-AAACTTCATTTCTAA
1 CAAATCTTCAAACTTCATTTCTAA
*
13904 CAACCTCTTCAAACTTCATTTCTAA
1 CAA-ATCTTCAAACTTCATTTCTAA
13929 CAAATCTTCAAA-TTCATTT
1 CAAATCTTCAAACTTCATTT
13948 TCCTTCATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
23 10 0.26
24 11 0.28
25 18 0.46
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.37
Consensus pattern (24 bp):
CAAATCTTCAAACTTCATTTCTAA
Found at i:13949 original size:24 final size:25
Alignment explanation
Indices: 13889--13947 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
13879 TTCAAATCCT
*
13889 AAACTTCATTTCTAACAACCTCTTC
1 AAACTTCATTTCTAACAACATCTTC
13914 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
13938 AAA-TTCATTT
1 AAACTTCATTT
13948 TCCTTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 18 0.55
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:26413 original size:24 final size:21
Alignment explanation
Indices: 26380--26440 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
26370 ACCCAAGTTA
* *
26380 TTGGCAATTTTTTATACTGTTGGG
1 TTGGCCATTTTTTATA-TGCT--G
*
26404 TTGGCCATTTTTAATATGCTG
1 TTGGCCATTTTTTATATGCTG
26425 TTGGCCATTTTTTATA
1 TTGGCCATTTTTTATA
26441 AGAAACGACT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 16 0.48
23 3 0.09
24 14 0.42
ACGTcount: A:0.18, C:0.11, G:0.20, T:0.51
Consensus pattern (21 bp):
TTGGCCATTTTTTATATGCTG
Found at i:27039 original size:36 final size:36
Alignment explanation
Indices: 26992--27061 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
26982 TTAGTCCAAC
26992 TTCAACTTTGATTCCCTTGATTGTGTAATTCTCGAG
1 TTCAACTTTGATTCCCTTGATTGTGTAATTCTCGAG
*
27028 TTCAACTTTGATTCCCTTGGTTGTGTAATTCTCG
1 TTCAACTTTGATTCCCTTGATTGTGTAATTCTCG
27062 GGAGTAGCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (36 bp):
TTCAACTTTGATTCCCTTGATTGTGTAATTCTCGAG
Found at i:34132 original size:20 final size:20
Alignment explanation
Indices: 34109--34147 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
34099 TTATTATGAT
34109 TTCTGA-TTTTTTATTATACG
1 TTCTGACTTTTTT-TTATACG
34129 TTCTGAGCTTTTTTTTATA
1 TTCTGA-CTTTTTTTTATA
34148 TGATTTCAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 5 0.29
22 6 0.35
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.62
Consensus pattern (20 bp):
TTCTGACTTTTTTTTATACG
Found at i:43467 original size:1 final size:1
Alignment explanation
Indices: 43461--43493 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
43451 ATAAGGTTGG
43461 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
43494 ATTGTGGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:46521 original size:11 final size:11
Alignment explanation
Indices: 46505--46536 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
46495 GTTACTAATC
46505 TCTTTCTTTTT
1 TCTTTCTTTTT
46516 TCTTTCTTTTT
1 TCTTTCTTTTT
46527 T-TTT-TTTTT
1 TCTTTCTTTTT
46536 T
1 T
46537 GATAAAAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 6 0.29
10 3 0.14
11 12 0.57
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TCTTTCTTTTT
Found at i:51435 original size:30 final size:30
Alignment explanation
Indices: 51395--51496 Score: 138
Period size: 30 Copynumber: 3.4 Consensus size: 30
51385 CATCAGAAAA
51395 GGGCTTATTTGGCCTTTTTAAAGAGTTCAG
1 GGGCTTATTTGGCCTTTTTAAAGAGTTCAG
* **
51425 GGGTTTATTTGG-C--TGCAATTAGAGTTCAG
1 GGGCTTATTTGGCCTTTTTAA--AGAGTTCAG
51454 GGGCTTATTTGGCCTTTTTAAAGAGTTCAG
1 GGGCTTATTTGGCCTTTTTAAAGAGTTCAG
51484 GGGCTTATTTGGC
1 GGGCTTATTTGGC
51497 TGCAATTAGA
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
27 3 0.05
29 21 0.34
30 34 0.56
32 3 0.05
ACGTcount: A:0.19, C:0.13, G:0.29, T:0.39
Consensus pattern (30 bp):
GGGCTTATTTGGCCTTTTTAAAGAGTTCAG
Found at i:51449 original size:29 final size:29
Alignment explanation
Indices: 51416--51523 Score: 148
Period size: 29 Copynumber: 3.7 Consensus size: 29
51406 GCCTTTTTAA
*
51416 AGAGTTCAGGGGTTTATTTGGCTGCAATT
1 AGAGTTCAGGGGCTTATTTGGCTGCAATT
**
51445 AGAGTTCAGGGGCTTATTTGGC--CTTTTT
1 AGAGTTCAGGGGCTTATTTGGCTGC-AATT
51473 AAAGAGTTCAGGGGCTTATTTGGCTGCAATT
1 --AGAGTTCAGGGGCTTATTTGGCTGCAATT
51504 AGAGTTCAGGGGCTTATTTG
1 AGAGTTCAGGGGCTTATTTG
51524 ACCGTTTTGT
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.01
28 2 0.03
29 41 0.59
30 22 0.32
31 2 0.03
32 1 0.01
ACGTcount: A:0.20, C:0.12, G:0.31, T:0.37
Consensus pattern (29 bp):
AGAGTTCAGGGGCTTATTTGGCTGCAATT
Found at i:51466 original size:59 final size:59
Alignment explanation
Indices: 51395--51523 Score: 249
Period size: 59 Copynumber: 2.2 Consensus size: 59
51385 CATCAGAAAA
*
51395 GGGCTTATTTGGCCTTTTTAAAGAGTTCAGGGGTTTATTTGGCTGCAATTAGAGTTCAG
1 GGGCTTATTTGGCCTTTTTAAAGAGTTCAGGGGCTTATTTGGCTGCAATTAGAGTTCAG
51454 GGGCTTATTTGGCCTTTTTAAAGAGTTCAGGGGCTTATTTGGCTGCAATTAGAGTTCAG
1 GGGCTTATTTGGCCTTTTTAAAGAGTTCAGGGGCTTATTTGGCTGCAATTAGAGTTCAG
51513 GGGCTTATTTG
1 GGGCTTATTTG
51524 ACCGTTTTGT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 69 1.00
ACGTcount: A:0.19, C:0.12, G:0.29, T:0.39
Consensus pattern (59 bp):
GGGCTTATTTGGCCTTTTTAAAGAGTTCAGGGGCTTATTTGGCTGCAATTAGAGTTCAG
Found at i:52343 original size:42 final size:40
Alignment explanation
Indices: 52275--52354 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 40
52265 CTTATTTTCT
52275 TAGGTTTAGGGGGCTGTTAAATATTAGGGTATTGATGTTA
1 TAGGTTTAGGGGGCTGTTAAATATTAGGGTATTGATGTTA
* * *
52315 TAGGTTTAGGGGTGGGTGTTAGATATTAGGGTTTTGATGT
1 TAGGTTTA-GGG-GGCTGTTAAATATTAGGGTATTGATGT
52355 AATATATGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 8 0.23
41 3 0.09
42 24 0.69
ACGTcount: A:0.21, C:0.01, G:0.36, T:0.41
Consensus pattern (40 bp):
TAGGTTTAGGGGGCTGTTAAATATTAGGGTATTGATGTTA
Found at i:66826 original size:2 final size:2
Alignment explanation
Indices: 66819--66849 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
66809 TAATTAAAAC
*
66819 TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
66850 TCTTGAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:66889 original size:49 final size:49
Alignment explanation
Indices: 66836--66934 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
66826 ATATATATAT
66836 ATATAAATATATATTCTTGAATAAATTGGTGTCCACTATATTAAAGGGA
1 ATATAAATATATATTCTTGAATAAATTGGTGTCCACTATATTAAAGGGA
66885 ATATAAATATATATTCTTGAATAAATTGGTGTCCACTATATTAAAGGGA
1 ATATAAATATATATTCTTGAATAAATTGGTGTCCACTATATTAAAGGGA
66934 A
1 A
66935 AAGCTATGCG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.36
Consensus pattern (49 bp):
ATATAAATATATATTCTTGAATAAATTGGTGTCCACTATATTAAAGGGA
Found at i:71825 original size:29 final size:29
Alignment explanation
Indices: 71793--71851 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
71783 GTGATCATCT
71793 GATGTTTAATTAATTGTAATTTTATGGTA
1 GATGTTTAATTAATTGTAATTTTATGGTA
71822 GATGTTTAATTAATTGTAATTTTATGGTA
1 GATGTTTAATTAATTGTAATTTTATGGTA
71851 G
1 G
71852 TGAACAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.51
Consensus pattern (29 bp):
GATGTTTAATTAATTGTAATTTTATGGTA
Found at i:72325 original size:33 final size:33
Alignment explanation
Indices: 72283--72349 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
72273 GAGAAATCAG
* *
72283 GCGGATAGAGTTGGAACTCTAAAACCTGCACAA
1 GCGGATAGAGTTGGAACTCCAAAACCAGCACAA
*
72316 GCGGATAGAGTTGGAACTCCAAAAGCAGCACAA
1 GCGGATAGAGTTGGAACTCCAAAACCAGCACAA
72349 G
1 G
72350 AATCTGCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.37, C:0.21, G:0.27, T:0.15
Consensus pattern (33 bp):
GCGGATAGAGTTGGAACTCCAAAACCAGCACAA
Done.