Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016058.1 Corchorus capsularis cultivar CVL-1 contig16079, 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: 19272
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Found at i:397 original size:31 final size:32
Alignment explanation
Indices: 354--415 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
344 CAATTTAGAA
*
354 ATATATTTTAAAAA-GGGTATAATCGAAAAAT
1 ATATATTTTAAAAAGGGGTACAATCGAAAAAT
* *
385 ATATTTTTTAAAAAGGGGTACAATCGGAAAA
1 ATATATTTTAAAAAGGGGTACAATCGAAAAA
416 CATAAAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.48, C:0.05, G:0.16, T:0.31
Consensus pattern (32 bp):
ATATATTTTAAAAAGGGGTACAATCGAAAAAT
Found at i:6470 original size:40 final size:40
Alignment explanation
Indices: 6426--6509 Score: 132
Period size: 40 Copynumber: 2.1 Consensus size: 40
6416 AAGGGTAAAC
* *
6426 ATGTAGTTTTATTTCATTTAGATTAATTAGTTATGTAATT
1 ATGTAGTTTTATTTCATTTAAATTAATTAGTTAGGTAATT
* *
6466 ATGTATTTTTATTTCATTTAAATTAATTATTTAGGTAATT
1 ATGTAGTTTTATTTCATTTAAATTAATTAGTTAGGTAATT
6506 ATGT
1 ATGT
6510 TTTATTCAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (40 bp):
ATGTAGTTTTATTTCATTTAAATTAATTAGTTAGGTAATT
Found at i:7936 original size:139 final size:138
Alignment explanation
Indices: 7789--8069 Score: 535
Period size: 139 Copynumber: 2.0 Consensus size: 138
7779 TCTATTTATG
*
7789 AGATGTTTTTCTTTTTGGCAATCTATTTATGAGATGTTAGTATAGTAAAGCTACTTAAGATATAA
1 AGATGTTTTTCTTTTTGGCAATCTATTTATGAGATGTTAGTATAGTAAAGCTACTAAAGATATAA
7854 GGTTACTGAATTTTTGATGATACTATAGTTTAGCCTTTTTTTTTAATAACCATAAATAAGAAATT
66 GGTTACTGAATTTTTGATGATACTATAGTTTAGCC-TTTTTTTTAATAACCATAAATAAGAAATT
7919 TGATAATTA
130 TGATAATTA
*
7928 AGATGTTTTTCTTTTTGGCAATCTATTTATGAGATGTTAGTATAGTAAAGTTACTAAAGATATAA
1 AGATGTTTTTCTTTTTGGCAATCTATTTATGAGATGTTAGTATAGTAAAGCTACTAAAGATATAA
7993 GGTTACTGAATTTTTGATGATACTATAGTTTAGCCTTTTTTTTAATAACCATAAATAAGAAATTT
66 GGTTACTGAATTTTTGATGATACTATAGTTTAGCCTTTTTTTTAATAACCATAAATAAGAAATTT
8058 GATAATTA
131 GATAATTA
8066 AGAT
1 AGAT
8070 TTCTAAGAAT
Statistics
Matches: 140, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
138 42 0.30
139 98 0.70
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (138 bp):
AGATGTTTTTCTTTTTGGCAATCTATTTATGAGATGTTAGTATAGTAAAGCTACTAAAGATATAA
GGTTACTGAATTTTTGATGATACTATAGTTTAGCCTTTTTTTTAATAACCATAAATAAGAAATTT
GATAATTA
Found at i:11083 original size:2 final size:2
Alignment explanation
Indices: 11078--11104 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11068 ACTTTACTAG
11078 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
11105 TTTGAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11475 original size:2 final size:2
Alignment explanation
Indices: 11470--11513 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
11460 ATTAGAGAGC
*
11470 AT AT AT AT AT AT AT AT AT AA 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 AT AT AT AT
11512 AT
1 AT
11514 TCATACCATC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13388 original size:20 final size:21
Alignment explanation
Indices: 13363--13402 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
13353 AAATACAAGG
13363 CATTTGATTTAC-AAATTGGA
1 CATTTGATTTACAAAATTGGA
*
13383 CATTTGATTTGCAAAATTGG
1 CATTTGATTTACAAAATTGG
13403 TGCTCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (21 bp):
CATTTGATTTACAAAATTGGA
Found at i:13971 original size:19 final size:19
Alignment explanation
Indices: 13947--13985 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
13937 ACTTTGCAGC
13947 ATGGATTTTACAATAGGAG
1 ATGGATTTTACAATAGGAG
13966 ATGGATTTTACAATAGGAG
1 ATGGATTTTACAATAGGAG
13985 A
1 A
13986 AAAGGGGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (19 bp):
ATGGATTTTACAATAGGAG
Found at i:15470 original size:51 final size:51
Alignment explanation
Indices: 15410--15578 Score: 239
Period size: 51 Copynumber: 3.3 Consensus size: 51
15400 GACCTTGACA
* * *
15410 ATAAAAATTGAATCTTTGTATAGTAAGGGTTGAGTTCTAGTAATTTTAGCC
1 ATAAAAATTGAATCTTTATGTAGTAAGGGTTGAGTTCTAGTAATTTTAACC
* *
15461 ATAAAAATTGAATCTTTATGTAGTAAAGGTTAAGTTCTAGTAATTTTAACC
1 ATAAAAATTGAATCTTTATGTAGTAAGGGTTGAGTTCTAGTAATTTTAACC
* * * * * *
15512 ATAAAAATTAAATCTTTATGTAGTAAGAGTTGGGTTTTAGTAATTCTAACA
1 ATAAAAATTGAATCTTTATGTAGTAAGGGTTGAGTTCTAGTAATTTTAACC
15563 ATAAAAATTGAATCTT
1 ATAAAAATTGAATCTT
15579 GATAGTTTTT
Statistics
Matches: 104, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 104 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.39
Consensus pattern (51 bp):
ATAAAAATTGAATCTTTATGTAGTAAGGGTTGAGTTCTAGTAATTTTAACC
Found at i:16409 original size:38 final size:38
Alignment explanation
Indices: 16368--16584 Score: 353
Period size: 38 Copynumber: 5.7 Consensus size: 38
16358 AAATTAGGAC
* * *
16368 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGC
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
16406 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
* * * *
16444 TAAAGTAATAGTAATTAGTAAAATTGATAATTAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
16482 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
*
16520 CAAAGTAAGAATAATTAGTAAAATTGATAATTAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
*
16558 CAAAGTAAGAATAATCAGCAAAATTGA
1 CAAAGTAAGAATAATCAGTAAAATTGA
16585 GAGTAAAAGA
Statistics
Matches: 165, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 165 1.00
ACGTcount: A:0.52, C:0.05, G:0.16, T:0.27
Consensus pattern (38 bp):
CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
Found at i:16877 original size:14 final size:14
Alignment explanation
Indices: 16854--16892 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
16844 GAGTTATATG
16854 GTAAAAAGTAATCA
1 GTAAAAAGTAATCA
*
16868 GTAAAGAGTAATCA
1 GTAAAAAGTAATCA
16882 GTAAAAAGTAA
1 GTAAAAAGTAA
16893 AAATGGCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21
Consensus pattern (14 bp):
GTAAAAAGTAATCA
Found at i:18776 original size:22 final size:22
Alignment explanation
Indices: 18748--18798 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
18738 TTAAATGATG
18748 ACGTGGACACCATGTAGACGCC
1 ACGTGGACACCATGTAGACGCC
* *
18770 ACGTGGACACCATGTGGATGCC
1 ACGTGGACACCATGTAGACGCC
18792 ACGTGGA
1 ACGTGGA
18799 TTTCATCCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.25, C:0.27, G:0.31, T:0.16
Consensus pattern (22 bp):
ACGTGGACACCATGTAGACGCC
Found at i:19209 original size:2 final size:2
Alignment explanation
Indices: 19202--19226 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19192 AGCTTCTTGC
19202 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
19227 GTGTGTGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.