Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007064.1 Corchorus capsularis cultivar CVL-1 contig07085, 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: 28582
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:2852 original size:20 final size:21
Alignment explanation
Indices: 2829--2872 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2819 TCATTTTGGG
*
2829 TTTTAATTCAAAATTTAATTT
1 TTTTAACTCAAAATTTAATTT
* *
2850 TTTTACCTGAAAATTTAATTT
1 TTTTAACTCAAAATTTAATTT
2871 TT
1 TT
2873 CGGGGGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTAACTCAAAATTTAATTT
Found at i:4365 original size:15 final size:15
Alignment explanation
Indices: 4342--4387 Score: 74
Period size: 15 Copynumber: 3.0 Consensus size: 15
4332 GCACATCTTG
4342 GTGGTATTTGAACTA
1 GTGGTATTTGAACTA
*
4357 GTTGTATTTGAACTTA
1 GTGGTATTTGAAC-TA
4373 GTGGTATTTGAACTA
1 GTGGTATTTGAACTA
4388 TTTAAATGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 14 0.50
16 14 0.50
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (15 bp):
GTGGTATTTGAACTA
Found at i:4379 original size:16 final size:16
Alignment explanation
Indices: 4342--4386 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
4332 GCACATCTTG
4342 GTGGTATTTGAAC-TA
1 GTGGTATTTGAACTTA
*
4357 GTTGTATTTGAACTTA
1 GTGGTATTTGAACTTA
4373 GTGGTATTTGAACT
1 GTGGTATTTGAACT
4387 ATTTAAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.44
Consensus pattern (16 bp):
GTGGTATTTGAACTTA
Found at i:6901 original size:34 final size:34
Alignment explanation
Indices: 6831--6903 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
6821 TTTTTTCTAT
* ** *
6831 ATATATAATTTAGACCTGATTTTATTTTTGAAAA
1 ATATATAATTTAGACATGATTTTATAATTCAAAA
**
6865 ATATATAATTTAGACATGATTTTATAATTCCTAA
1 ATATATAATTTAGACATGATTTTATAATTCAAAA
6899 ATATA
1 ATATA
6904 ATTACATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (34 bp):
ATATATAATTTAGACATGATTTTATAATTCAAAA
Found at i:6905 original size:13 final size:13
Alignment explanation
Indices: 6887--6931 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
6877 GACATGATTT
6887 TATAATTCCTAAA
1 TATAATTCCTAAA
* *
6900 TATAATTAC-ATA
1 TATAATTCCTAAA
*
6912 TATAATTCCTAGA
1 TATAATTCCTAAA
6925 TATAATT
1 TATAATT
6932 TCATTACATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.42
Consensus pattern (13 bp):
TATAATTCCTAAA
Found at i:7088 original size:44 final size:42
Alignment explanation
Indices: 7015--7105 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 42
7005 TTTTATTACC
*
7015 TATATAATTTCTAAATACTATTATTTTCTAATTATAATTT-T
1 TATAAAATTTCTAAATACTATTATTTTCTAATTATAATTTCT
7056 TATAAAATTTCTAAATACTACTATTATTTTCTAATTATAATTTCT
1 TATAAAATTTCT-AA-A-TACTATTATTTTCTAATTATAATTTCT
7101 TATAA
1 TATAA
7106 GTAGCGGGCT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
41 11 0.24
42 2 0.04
43 1 0.02
44 25 0.56
45 6 0.13
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (42 bp):
TATAAAATTTCTAAATACTATTATTTTCTAATTATAATTTCT
Found at i:8076 original size:33 final size:33
Alignment explanation
Indices: 8034--8106 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
8024 TTATAACATC
8034 AATTTTGGGTGCTCAAAATATACTCTTAAATTG
1 AATTTTGGGTGCTCAAAATATACTCTTAAATTG
*
8067 AATTTTGGGTGCTGAAAATATACTCTTAAATTG
1 AATTTTGGGTGCTCAAAATATACTCTTAAATTG
8100 AATTTTG
1 AATTTTG
8107 TGTTGTTTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (33 bp):
AATTTTGGGTGCTCAAAATATACTCTTAAATTG
Found at i:11312 original size:24 final size:24
Alignment explanation
Indices: 11285--11371 Score: 129
Period size: 24 Copynumber: 3.6 Consensus size: 24
11275 ACACTTTAAT
* *
11285 ATAGCGGTGTTTAGACGCCTCTAA
1 ATAGCGGCGTTTAGACGTCTCTAA
11309 ATAGCGGCGTTTAGACGTCTCTAA
1 ATAGCGGCGTTTAGACGTCTCTAA
*
11333 ATAGCGGCATTTAGACGTCTCTAA
1 ATAGCGGCGTTTAGACGTCTCTAA
* *
11357 ATAGCAGCGTCTAGA
1 ATAGCGGCGTTTAGA
11372 TGCCGTTATA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (24 bp):
ATAGCGGCGTTTAGACGTCTCTAA
Found at i:15158 original size:16 final size:16
Alignment explanation
Indices: 15137--15173 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
15127 TTTATCTATA
*
15137 TGCTTGCTATAGTATG
1 TGCTTGCTATAGGATG
15153 TGCTTGCTATAGGATG
1 TGCTTGCTATAGGATG
15169 T-CTTG
1 TGCTTG
15174 AATGATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.16, C:0.14, G:0.27, T:0.43
Consensus pattern (16 bp):
TGCTTGCTATAGGATG
Found at i:20405 original size:20 final size:21
Alignment explanation
Indices: 20376--20429 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
20366 TTGGTTTTTA
20376 TTCT-TTTGTTTTCG-TATCT
1 TTCTATTTGTTTTCGATATCT
*
20395 TTCTATTTGTTCTCGATATCT
1 TTCTATTTGTTTTCGATATCT
20416 TTCTATTTAGTTTT
1 TTCTATTT-GTTTT
20430 TCTTTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 4 0.13
20 9 0.30
21 13 0.43
22 4 0.13
ACGTcount: A:0.11, C:0.15, G:0.09, T:0.65
Consensus pattern (21 bp):
TTCTATTTGTTTTCGATATCT
Found at i:22284 original size:439 final size:439
Alignment explanation
Indices: 21458--22397 Score: 1389
Period size: 439 Copynumber: 2.1 Consensus size: 439
21448 GATTAAATGA
* * * * *
21458 CATAAAACATAAAAGTAT-GAGGATCATTTGATAGATAATCCAACAAAAAAAATATTTTTTTATG
1 CATAAAGCATAAAAGTATAG-GGATCATTTGATAAATAATCCAGCAAAAAAATTATTTGTTTATG
* * * *
21522 GAGATCAAACATAAAAATTCTCTCTCGAACCTTCCACGAAACTCATTAATCAAATTCAGCTTTCA
65 GAAACCAAACATAAAAATTCCCTCTCGAACCCTCCACGAAACTCATTAATCAAATTCAGCTTTCA
* *
21587 AACCCTTAACGAAAGTCGTAGATCATACAATAACCTTTTAATCGACACTTAAACAACCTCAATCA
130 AACCCTTAACGAAAGTCGTAGATCACACAATAACCTTTTAACCGACACTTAAACAACCTCAATCA
* *
21652 GACAAGTGGACCGAAAATTATACAATATTAAATTGACCGGCAATGGAAACCACAAAATCTCAAAA
195 GACAAGTGGACCGAAAATTATACAATATCAAATTGACCGGCAATCGAAACCACAAAATCTCAAAA
* * *
21717 GTACTTTTTAGATTCAAAACATTAAAATTGACTTTTGAGTCCTTTATGAAAGTTGTAGATCATGA
260 GCACTTTTTAGAATCAAAACATTAAAATTGACTTTTGAGTCCTTCATGAAAGTTGTAGATCATGA
* *
21782 AATTACCTTTTAATAGACACTTGAATCACCTTGATCGGACAAGAAAACAAAAAATAAAAGAATTA
325 AATTACCTTTTAATAGACACTTGAATCACCTTCATCGGACAACAAAACAAAAAATAAAAGAATTA
* *
21847 AAGCCGAAACGTTCAATCGTCCAACCCAGAATTTGTGAGGGACTAAATAC
390 AAGCCGAAACGTTCAATCGTCCAACCCAAAAATTGTGAGGGACTAAATAC
**
21897 CATAAATTATAAAAGTATAGGGATCATTTGATAAATAATCCAGCAAAAAAATTATTTGTTTATGG
1 CATAAAGCATAAAAGTATAGGGATCATTTGATAAATAATCCAGCAAAAAAATTATTTGTTTATGG
* * *
21962 AAACCAAACATAAAAATTCCCTCTTGAACCCTCCACGAAACTCATTAATCAAATTCAGCTTTTAG
66 AAACCAAACATAAAAATTCCCTCTCGAACCCTCCACGAAACTCATTAATCAAATTCAGCTTTCAA
* * *
22027 GCCC-TAATGAAAG-CTGTAGATCACACAATAACCTTTTAACCGACACTTGAACAACCTCAAT-A
131 ACCCTTAACGAAAGTC-GTAGATCACACAATAACCTTTTAACCGACACTTAAACAACCTCAATCA
* * * *
22089 GGACAAGTGGACCGAAATTTATACAATATCAAATAT-ACCGGCAATCGAGATCACAAAATTTCAG
195 -GACAAGTGGACCGAAAATTATACAATATCAAAT-TGACCGGCAATCGAAACCACAAAATCTCA-
22153 AAA-CAC-TTTT-GAATCAAAACATTAAAATTGACTTTTGAGTCCTTCATGGAAA-TTGTAGATC
257 AAAGCACTTTTTAGAATCAAAACATTAAAATTGACTTTTGAGTCCTTCAT-GAAAGTTGTAGATC
*
22214 ATGAAATTACCTTTTATTAGACACTTGAATCACCTTCATCGGACAAACAAAACAAAAAAAATAAA
321 ATGAAATTACCTTTTAATAGACACTTGAATCACCTTCATCGGAC-AACAAAAC--AAAAAATAAA
* *
22279 AGAATTAAAGGCGAAACGTTCAATCGTCCAACCCAAAAATTGTGAGGGACTAAATAG
383 AGAATTAAAGCCGAAACGTTCAATCGTCCAACCCAAAAATTGTGAGGGACTAAATAC
*
22336 CATAAAGCATAAAAGTATAGGGATCATTTGATAAATAGA-CCAG-AAAAAAATGATTTGTTTAT
1 CATAAAGCATAAAAGTATAGGGATCATTTGATAAATA-ATCCAGCAAAAAAATTATTTGTTTAT
22398 TATAAGCGGG
Statistics
Matches: 454, Mismatches: 37, Indels: 21
0.89 0.07 0.04
Matches are distributed among these distances:
436 86 0.19
437 17 0.04
438 125 0.28
439 224 0.49
440 2 0.00
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.27
Consensus pattern (439 bp):
CATAAAGCATAAAAGTATAGGGATCATTTGATAAATAATCCAGCAAAAAAATTATTTGTTTATGG
AAACCAAACATAAAAATTCCCTCTCGAACCCTCCACGAAACTCATTAATCAAATTCAGCTTTCAA
ACCCTTAACGAAAGTCGTAGATCACACAATAACCTTTTAACCGACACTTAAACAACCTCAATCAG
ACAAGTGGACCGAAAATTATACAATATCAAATTGACCGGCAATCGAAACCACAAAATCTCAAAAG
CACTTTTTAGAATCAAAACATTAAAATTGACTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAA
ATTACCTTTTAATAGACACTTGAATCACCTTCATCGGACAACAAAACAAAAAATAAAAGAATTAA
AGCCGAAACGTTCAATCGTCCAACCCAAAAATTGTGAGGGACTAAATAC
Found at i:23615 original size:441 final size:444
Alignment explanation
Indices: 22782--23921 Score: 1322
Period size: 441 Copynumber: 2.6 Consensus size: 444
22772 CCCGCTTATA
*
22782 ATAAACAAATCA--TTTTTTGCTGGTTTATTTATCAAATGATCC-CTATACTTTTATGCTTTATG
1 ATAAACAAAT-ATTTTTTTTGCTGGATTATTTATCAAATGATCCTC-ATACTTTTATGCTTTATG
* * * *
22844 CTATTTAGTCC-CT-CAGAATTTCTGGGTTGGACAACTGAACGTTTCGGCTTT-GATTCTTTTAT
64 CTATTTAATCCTTTACA-AATTT-TGGGTTGGACAATTTAACGTTTCGGCTTTAG-TTCTTTTAT
* * * *
22906 TTTTTATTTTGCTTGTCCGATCAAGGTGATTCAAGTGTATATTAAAAGGTAATTTCATGATCTAC
126 TTTTTGTTTTACTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATTTAC
* * * * * *
22971 AACTTTCGTGAAGGACTCAAAAGTCATTTTTAATGTGTTGATTCAAAACAATGCTTCTAAAATTT
191 AACTTTCGTGAAGGACTCAAAAGTCAATATTAAGGTGTTCATTCAAAAAAATGCTTCCAAAATTT
* * * * * ** * * *
23036 TGTGGTCTCAATTGCCGGTCTCTCTGATATTTTATAATTTTCTGTCCGCTTGCCCGATTGAGATT
256 GGTGGTCTCAATTACCAGTCTATCTAATATCGTATAAATTTCTGTCCACGTGCCCGATTGAGATT
* *
23101 GTTCAAGTGTCGATTAAAAGGTTATTCTGTGATCTACGACTTTCGTTAAGGGTCTAAAAGCTGAA
321 GTTCAAGTGTCGATTAAAAGGTTATTCTGTGATCTACGACTTTCGTCAAGGGTCCAAAAGCTGAA
* * **
23166 TTTGATTAATGAGTTTC-G-T-G-GAGGGTTCGAGAGAGAACTTTTATGTTTGGTCTCC
386 TTTGATTAATGAGTTTCAGTTCGAGAGGGTTCAAGAGAGAACTTTTATGTCTAATCTCC
23221 ATAAACAAATATTTTTTTTGCTGGATTATTTATCAAATGATCCTCATACTTTTATGCTTTATGCT
1 ATAAACAAATATTTTTTTTGCTGGATTATTTATCAAATGATCCTCATACTTTTATGCTTTATGCT
*
23286 ATTTAATCCTTTACAAATTTTGGGTTGGACGATTTAACGTTTCGGCTTTAGTTCTTTTATTTTTT
66 ATTTAATCCTTTACAAATTTTGGGTTGGACAATTTAACGTTTCGGCTTTAGTTCTTTTA-TTTTT
* * * * *
23351 TGTTTTACTTATCCAATTAAGGTGATTCAAGTGTCTATTTAAAGGTAATTTAATGATTTACAACT
130 TGTTTTACTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATTTACAACT
* ** *
23416 TTCGTTAAGTTCTCAAAAGTCAATATTGAGGT-TTCAGTTCAAAAAAATGCTTCCAAAATTTGGT
195 TTCGTGAAGGACTCAAAAGTCAATATTAAGGTGTTCA-TTCAAAAAAATGCTTCCAAAATTTGGT
* * * * *
23480 GGTCTCGATTACTAGTCTATTTAATATCGTATAAATTT-TGATCCACGTGTCCGATTGAGGTTGT
259 GGTCTCAATTACCAGTCTATCTAATATCGTATAAATTTCTG-TCCACGTGCCCGATTGAGATTGT
* * * ** *
23544 TCAAGTGTCGGTTAAAAGGTTATTGTGTGATTTGTGACTTTCGTCAAGGGTCCCAAAGCTGAATT
323 TCAAGTGTCGATTAAAAGGTTATTCTGTGATCTACGACTTTCGTCAAGGGTCCAAAAGCTGAATT
* * *
23609 TGATTAATGAGTTTCATTGAAGGTTCGAGAGGGTTCAAGAGGGAATTTTTATGTCTAATCTCT
388 TGATTAATGAGTTTC-----A-GTTCGAGAGGGTTCAAGAGAGAACTTTTATGTCTAATCTCC
*
23672 ATAAACAAATATTTTTTTTGCTGGATTATTTATCAAATGATCCTCATACTTTTTATGTTTTATGC
1 ATAAACAAATATTTTTTTTGCTGGATTATTTATCAAATGATCCTCATAC-TTTTATGCTTTATGC
* * * * *
23737 TATTTATTCCTTTAC-AATTATGGGTTGGACTATTTAACGCTTCGTCTTTTA-TT-TTTGTATTT
65 TATTTAATCCTTTACAAATTTTGGGTTGGACAATTTAACGTTTCGGC-TTTAGTTCTTT-TATTT
* * * * **
23799 TATGTTCTATTTGTCTGATCAAGGTGATTCAAGTGTCTAAGAAAAGGTAATTTCATGATTTACAA
128 TTTGTTTTACTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATTTACAA
* * * * * * * * *
23864 CTTTCATGAA-AAGCTCAGAAGCCAATTTTAATGTTTTAATTCTAAAAAATGCTTCCAA
193 CTTTCGTGAAGGA-CTCAAAAGTCAATATTAAGGTGTTCATTCAAAAAAATGCTTCCAA
23922 TTGTATTTTG
Statistics
Matches: 594, Mismatches: 83, Indels: 37
0.83 0.12 0.05
Matches are distributed among these distances:
438 1 0.00
439 10 0.02
440 96 0.16
441 237 0.40
442 2 0.00
448 1 0.00
449 1 0.00
450 103 0.17
451 111 0.19
452 32 0.05
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (444 bp):
ATAAACAAATATTTTTTTTGCTGGATTATTTATCAAATGATCCTCATACTTTTATGCTTTATGCT
ATTTAATCCTTTACAAATTTTGGGTTGGACAATTTAACGTTTCGGCTTTAGTTCTTTTATTTTTT
GTTTTACTTGTCCGATCAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATTTACAACTT
TCGTGAAGGACTCAAAAGTCAATATTAAGGTGTTCATTCAAAAAAATGCTTCCAAAATTTGGTGG
TCTCAATTACCAGTCTATCTAATATCGTATAAATTTCTGTCCACGTGCCCGATTGAGATTGTTCA
AGTGTCGATTAAAAGGTTATTCTGTGATCTACGACTTTCGTCAAGGGTCCAAAAGCTGAATTTGA
TTAATGAGTTTCAGTTCGAGAGGGTTCAAGAGAGAACTTTTATGTCTAATCTCC
Found at i:24159 original size:19 final size:21
Alignment explanation
Indices: 24133--24177 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
24123 TAATTAAATT
*
24133 AAAC-ATAATTAA-TAGA-CA
1 AAACTATAATAAATTAGATCA
24151 AAACTATAATAAATTAGATCA
1 AAACTATAATAAATTAGATCA
24172 AAACTA
1 AAACTA
24178 ATTTAATCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 7 0.30
20 4 0.17
21 8 0.35
ACGTcount: A:0.60, C:0.11, G:0.04, T:0.24
Consensus pattern (21 bp):
AAACTATAATAAATTAGATCA
Found at i:27617 original size:21 final size:21
Alignment explanation
Indices: 27591--27633 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
27581 AAAAAATAAA
27591 TAAATAAATAAACCTCAATTG
1 TAAATAAATAAACCTCAATTG
27612 TAAATAAATAAACCTCAATTG
1 TAAATAAATAAACCTCAATTG
27633 T
1 T
27634 CCTCATCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (21 bp):
TAAATAAATAAACCTCAATTG
Done.