Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015781.1 Corchorus capsularis cultivar CVL-1 contig15802, 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: 44404
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Found at i:4257 original size:2 final size:2
Alignment explanation
Indices: 4250--4292 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
4240 TATGCTTTAC
*
4250 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT -T AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
4292 A
1 A
4293 AACAAATCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11095 original size:25 final size:25
Alignment explanation
Indices: 11058--11107 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
11048 TCACATGGTA
*
11058 AAAACGAATTTATTAAATAAATTCC
1 AAAACGAAATTATTAAATAAATTCC
*
11083 AAAATGAAATTATTAAATAAATTCC
1 AAAACGAAATTATTAAATAAATTCC
11108 TATAGACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.32
Consensus pattern (25 bp):
AAAACGAAATTATTAAATAAATTCC
Found at i:16631 original size:13 final size:13
Alignment explanation
Indices: 16613--16637 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16603 TTTAAAATCA
16613 AAATAATATTTAT
1 AAATAATATTTAT
16626 AAATAATATTTA
1 AAATAATATTTA
16638 GAACATTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATAATATTTAT
Found at i:17996 original size:161 final size:160
Alignment explanation
Indices: 17690--18009 Score: 362
Period size: 161 Copynumber: 2.0 Consensus size: 160
17680 TTAATTAAAA
* ** * *
17690 TTTGGACTCCACAAGCGGGTTGAGGAGTTGACATGTGTCTATTTTCTGAATTAATTAAATTTTAA
1 TTTGGACTACACAAGCGGAATGAGGAGTTGACACGTCTCTATTTTCTGAATTAATTAAATTTTAA
* * *
17755 ATATTTCAATCTAGTCCCTAAGGACACATGTCACCCTTTTAGACCCGCATGTGCAGTCTCCTAAA
66 ATATTTCAAACTAGTCCCTAAGGACACATGTCACCC-TTTAGACCCACATGTACAGTCTCCTAAA
* * *
17820 TTCCACTTGACAGTGTATTGAATAATTTTCC
130 CTCCACTTAACAGTGTATAGAATAATTTTCC
***
17851 TTTGGACTACACAAGCGGAATGAGGAGTTGACACGTACTC-ATTTTCTGAATTAATTTTGTTTTT
1 TTTGGACTACACAAGCGGAATGAGGAGTTGACACGT-CTCTATTTTCTGAATTAA-TTAAATTTT
* * * *
17915 AAA-A-TTCAAAACTATTCTCTAAAGGACACATGTCAACCC-TTAGACTCCACATGTATAGTCTG
64 AAATATTTC-AAACTAGTCCCT-AAGGACACATGTC-ACCCTTTAGAC-CCACATGTACAGTCTC
* *
17977 TTAAACTCCAC-TAACAGTGTATAGTATAATTTT
125 CTAAACTCCACTTAACAGTGTATAGAATAATTTT
18010 TCATATAAAA
Statistics
Matches: 133, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
160 3 0.02
161 81 0.61
162 45 0.34
163 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (160 bp):
TTTGGACTACACAAGCGGAATGAGGAGTTGACACGTCTCTATTTTCTGAATTAATTAAATTTTAA
ATATTTCAAACTAGTCCCTAAGGACACATGTCACCCTTTAGACCCACATGTACAGTCTCCTAAAC
TCCACTTAACAGTGTATAGAATAATTTTCC
Found at i:19914 original size:15 final size:15
Alignment explanation
Indices: 19890--19919 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19880 TCTCTTCATT
*
19890 TTTATTTTATTTATA
1 TTTATATTATTTATA
19905 TTTATATTATTTATA
1 TTTATATTATTTATA
19920 CTAGAACTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATATTATTTATA
Found at i:21417 original size:23 final size:23
Alignment explanation
Indices: 21387--21432 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
21377 CAAACAATCT
21387 TGAGCACTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
21410 TGAGCACTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
21433 CAAACTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.35, G:0.22, T:0.30
Consensus pattern (23 bp):
TGAGCACTCTCGCTCGGTCTCTA
Found at i:22346 original size:23 final size:23
Alignment explanation
Indices: 22316--22361 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
22306 CAAACAATCT
22316 TGAGCACTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
22339 TGAGCACTCTCGCTCGGTCTCTA
1 TGAGCACTCTCGCTCGGTCTCTA
22362 CAAACTAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.35, G:0.22, T:0.30
Consensus pattern (23 bp):
TGAGCACTCTCGCTCGGTCTCTA
Found at i:31158 original size:33 final size:32
Alignment explanation
Indices: 31121--31227 Score: 106
Period size: 33 Copynumber: 3.2 Consensus size: 32
31111 CGCCAAGCGA
* *
31121 TGGCCGGTTGTGGCTGGACATGTCCATGTCGCG
1 TGGCCGGTTGTGGCCGGACATCTCCA-GTCGCG
* *
31154 TGGCCGGTGGTGGCCGGGCATCTCCGAGTCGCG
1 TGGCCGGTTGTGGCCGGACATCTCC-AGTCGCG
* * * * *
31187 TGGCCAGTTTTGGCCGGTCTTCTCCAAGTCGCA
1 TGGCCGGTTGTGGCCGGACATCTCC-AGTCGCG
31220 TGGCCGGT
1 TGGCCGGT
31228 CACTCGCACC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 60 0.98
34 1 0.02
ACGTcount: A:0.08, C:0.28, G:0.38, T:0.25
Consensus pattern (32 bp):
TGGCCGGTTGTGGCCGGACATCTCCAGTCGCG
Found at i:31674 original size:38 final size:36
Alignment explanation
Indices: 31623--31696 Score: 103
Period size: 38 Copynumber: 2.0 Consensus size: 36
31613 CCAGTATTAA
* * *
31623 TTTTTTTTCAAAGAGGTTCATAAGTAAATTTCTTTT
1 TTTTTTTTCAAAGAGGATAATAAGCAAATTTCTTTT
31659 TTTTTTTTACAAAAGAGGATAATAAGCAAATTTCTTTT
1 TTTTTTTT-C-AAAGAGGATAATAAGCAAATTTCTTTT
31697 GTCAGAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 8 0.24
37 1 0.03
38 24 0.73
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (36 bp):
TTTTTTTTCAAAGAGGATAATAAGCAAATTTCTTTT
Found at i:32272 original size:23 final size:22
Alignment explanation
Indices: 32246--32288 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
32236 ATACTTTCAT
32246 GATATAATTTTGCAATCAATTGA
1 GATATAATTTTGCAAT-AATTGA
*
32269 GATATAATTTTGTAATAATT
1 GATATAATTTTGCAATAATT
32289 TGTCATATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.44
Consensus pattern (22 bp):
GATATAATTTTGCAATAATTGA
Found at i:32303 original size:16 final size:16
Alignment explanation
Indices: 32282--32318 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
32272 ATAATTTTGT
*
32282 AATAATTTGTCATATC
1 AATAATTTGTCAGATC
32298 AATAATTTGTCAGATC
1 AATAATTTGTCAGATC
32314 AATAA
1 AATAA
32319 CATCAATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (16 bp):
AATAATTTGTCAGATC
Found at i:33092 original size:2 final size:2
Alignment explanation
Indices: 33087--33118 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
33077 TGTGTGTGTG
*
33087 TA TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33119 CTAATATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:34291 original size:2 final size:2
Alignment explanation
Indices: 34284--34317 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
34274 GTGAGATGTG
34284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34318 TAGGATACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34713 original size:29 final size:30
Alignment explanation
Indices: 34665--34726 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
34655 GAGTTTTTGA
*
34665 CCAAACTATTATAGTTTTTAAAAATAATTC
1 CCAAACCATTATAGTTTTTAAAAATAATTC
* *
34695 CCAAACCATTGTA-TTTTTAAAATTAATTC
1 CCAAACCATTATAGTTTTTAAAAATAATTC
34724 CCA
1 CCA
34727 TTACAATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.40, C:0.18, G:0.03, T:0.39
Consensus pattern (30 bp):
CCAAACCATTATAGTTTTTAAAAATAATTC
Found at i:34736 original size:29 final size:29
Alignment explanation
Indices: 34679--34739 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
34669 ACTATTATAG
*
34679 TTTTTAAAAATAATTCCCAAACCATTGTA
1 TTTTTAAAAATAATTCCCAAACCAATGTA
* *
34708 TTTTTAAAATTAATTCCCATTA-CAATGTA
1 TTTTTAAAAATAATTCCCA-AACCAATGTA
34737 TTT
1 TTT
34740 CTTGTCGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (29 bp):
TTTTTAAAAATAATTCCCAAACCAATGTA
Found at i:36805 original size:21 final size:21
Alignment explanation
Indices: 36756--36797 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
36746 TCTCCACTAC
36756 CTGCACAGCAAAATTCTAATA
1 CTGCACAGCAAAATTCTAATA
**
36777 CTGCACAGCAAGTTTCTAATA
1 CTGCACAGCAAAATTCTAATA
36798 TTGTACAGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (21 bp):
CTGCACAGCAAAATTCTAATA
Done.