Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168371.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_590, 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: 22090
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Found at i:7025 original size:20 final size:20
Alignment explanation
Indices: 7000--7045 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
6990 TATATGTATT
7000 TGCTTGATCTTATCAAGATA
1 TGCTTGATCTTATCAAGATA
*
7020 TGCTTGATCTTATCAGGATA
1 TGCTTGATCTTATCAAGATA
7040 TGCTTG
1 TGCTTG
7046 GGCTTAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (20 bp):
TGCTTGATCTTATCAAGATA
Found at i:7051 original size:20 final size:20
Alignment explanation
Indices: 7000--7051 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
6990 TATATGTATT
*
7000 TGCTTGATCTTATCAAGATA
1 TGCTTGAGCTTATCAAGATA
* *
7020 TGCTTGATCTTATCAGGATA
1 TGCTTGAGCTTATCAAGATA
*
7040 TGCTTGGGCTTA
1 TGCTTGAGCTTA
7052 ACATAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.40
Consensus pattern (20 bp):
TGCTTGAGCTTATCAAGATA
Found at i:10678 original size:16 final size:16
Alignment explanation
Indices: 10657--10687 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10647 ATTACCTTAG
10657 AAAGGTTGAGAGTGAT
1 AAAGGTTGAGAGTGAT
10673 AAAGGTTGAGAGTGA
1 AAAGGTTGAGAGTGA
10688 ATGAAAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.23
Consensus pattern (16 bp):
AAAGGTTGAGAGTGAT
Found at i:11266 original size:39 final size:38
Alignment explanation
Indices: 11168--11301 Score: 128
Period size: 39 Copynumber: 3.4 Consensus size: 38
11158 TGGTTGCTTA
* *
11168 TTTATTTTTAAATTTGTGTGCCTCTATTAATTGGAGCC
1 TTTATTTTTAAAGTTGTGTGCCTCTATTAATAGGAGCC
*
11206 TTTATTTTTAAAAGTTATGTGCCTCTATT-ATAGAGAAG-C
1 TTTATTTTT-AAAGTTGTGTGCCTCTATTAATAG-G-AGCC
* * ** *
11245 TCTTATTTTTAAAGATGTGTGCCTCTGTTAGGAAGAGCCC
1 T-TTATTTTTAAAGTTGTGTGCCTCTATTAATAGGAG-CC
*
11285 TTTATTTTTCAAGTTGT
1 TTTATTTTTAAAGTTGT
11302 TGAGCCTTTG
Statistics
Matches: 78, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
38 14 0.18
39 51 0.65
40 13 0.17
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (38 bp):
TTTATTTTTAAAGTTGTGTGCCTCTATTAATAGGAGCC
Found at i:11944 original size:335 final size:335
Alignment explanation
Indices: 11323--11997 Score: 1192
Period size: 335 Copynumber: 2.0 Consensus size: 335
11313 TTAGAAGAGC
*
11323 TTTTTATAAATTTTTATATTTTTAAAAGTTATTGAACCTTTATTGAGAGGAGCTTTTTATATTTT
1 TTTTTATAAATTTTTATATTTTTAAAAGTTATTGAACCTCTATTGAGAGGAGCTTTTTATATTTT
*
11388 CAAAGTGTTAAGCCTCTATTTAGAGGAGTTTTTATGTTATACAAAAAGTCTAAGTGTCTGTTTTA
66 CAAAGTGTTAAGCCTCTATTTAGAGGAGTTTTTATGTTATACAAAAAGTCTAAGTGTCTATTTTA
11453 AAAGAATTTCAAAAAAATTGTCAAGTTGATTATCTGGATATGTGGGCTGCTACATCTTTGCATAA
131 AAAGAATTTCAAAAAAATTGTCAAGTTGATTATCTGGATATGTGGGCTGCTACATCTTTGCATAA
* * * * *
11518 TTACTGTTTAATAAAAAGTGTATAAATATGGGCAACTGTAGACACCCTAATTTGTTTGAAATTGT
196 TTACTATTTAATAAAAAATGCATAAAAATGGGCAACTGTAGACACCCTAATTTATTTGAAATTGT
*
11583 AATTGTTTTTTTTTAATGTTAAAAAATGAAAAAATTAGGAAAGTTT-GGGCCGGTTGAGTTTATC
261 AATTGATTTTTTTTAATGTTAAAAAATGAAAAAATTAGGAAAGTTTAGGG-CGGTTGAGTTTATC
11647 TGAGATTTTTT
325 TGAGATTTTTT
*
11658 TTTTTATAAATTTTTATATTTTTAAAAGTTATTGAGCCTCTATTGAGAGGAGCTTTTTATATTTT
1 TTTTTATAAATTTTTATATTTTTAAAAGTTATTGAACCTCTATTGAGAGGAGCTTTTTATATTTT
* *
11723 CAAAGTGTTAAGCTTTTATTTAGAGGAGTTTTTATGTTATACAAAAAGTCTAAGTGTCTATTTTA
66 CAAAGTGTTAAGCCTCTATTTAGAGGAGTTTTTATGTTATACAAAAAGTCTAAGTGTCTATTTTA
11788 AAAGAATTTCAAAAAAATTGTCAAGTTGATTATCTGGATATGTGGGCTGCTACATCTTTGCATAA
131 AAAGAATTTCAAAAAAATTGTCAAGTTGATTATCTGGATATGTGGGCTGCTACATCTTTGCATAA
* *
11853 TTACTATTTCATAAAAAATGCGTAAAAATGGGCAACTGTAGACACCCTAATTTATTTGAAATTGT
196 TTACTATTTAATAAAAAATGCATAAAAATGGGCAACTGTAGACACCCTAATTTATTTGAAATTGT
*
11918 AATT-ATTTTTTTTAATGTTAAAAAAATGAAAAAATTAGGAAAGTTTAGGGTGGTTGAGTTTATC
261 AATTGATTTTTTTTAATGTT-AAAAAATGAAAAAATTAGGAAAGTTTAGGGCGGTTGAGTTTATC
11982 TGAGATTTTTT
325 TGAGATTTTTT
11993 TTTTT
1 TTTTT
11998 TTGGATTATA
Statistics
Matches: 324, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
334 14 0.04
335 307 0.95
336 3 0.01
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.42
Consensus pattern (335 bp):
TTTTTATAAATTTTTATATTTTTAAAAGTTATTGAACCTCTATTGAGAGGAGCTTTTTATATTTT
CAAAGTGTTAAGCCTCTATTTAGAGGAGTTTTTATGTTATACAAAAAGTCTAAGTGTCTATTTTA
AAAGAATTTCAAAAAAATTGTCAAGTTGATTATCTGGATATGTGGGCTGCTACATCTTTGCATAA
TTACTATTTAATAAAAAATGCATAAAAATGGGCAACTGTAGACACCCTAATTTATTTGAAATTGT
AATTGATTTTTTTTAATGTTAAAAAATGAAAAAATTAGGAAAGTTTAGGGCGGTTGAGTTTATCT
GAGATTTTTT
Found at i:17435 original size:18 final size:18
Alignment explanation
Indices: 17409--17453 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
17399 GTGTCTATTA
*
17409 GGCCGTTAAATTGGTATAG
1 GGCC-TTAAATTGATATAG
* *
17428 GGCCTTAAATTGATTTTG
1 GGCCTTAAATTGATATAG
17446 GGCCTTAA
1 GGCCTTAA
17454 GTCTAGTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (18 bp):
GGCCTTAAATTGATATAG
Found at i:17549 original size:12 final size:12
Alignment explanation
Indices: 17517--17554 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
17507 CATTTCTTTT
*
17517 TTAATT-AAATA
1 TTAATTAAAAAA
17528 TTAA-TAAAAAA
1 TTAATTAAAAAA
17539 TTAATTAAAAAA
1 TTAATTAAAAAA
17551 TTAA
1 TTAA
17555 AAAATAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 1 0.04
11 12 0.50
12 11 0.46
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TTAATTAAAAAA
Found at i:17558 original size:22 final size:22
Alignment explanation
Indices: 17517--17558 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
17507 CATTTCTTTT
*
17517 TTAATTAAATATTAATAAAAAA
1 TTAATTAAAAATTAATAAAAAA
17539 TTAATTAAAAAATTAA-AAAA
1 TTAATT-AAAAATTAATAAAA
17559 TAAGAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TTAATTAAAAATTAATAAAAAA
Found at i:18423 original size:4 final size:4
Alignment explanation
Indices: 18409--18450 Score: 57
Period size: 4 Copynumber: 10.0 Consensus size: 4
18399 TTTTATATGC
*
18409 TTAT CTTAT TTAT TTATT TTAT TTAC TTAT TTAT TTAT TTAT
1 TTAT -TTAT TTAT TTA-T TTAT TTAT TTAT TTAT TTAT TTAT
18451 CTACTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
4 26 0.76
5 8 0.24
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:18437 original size:21 final size:20
Alignment explanation
Indices: 18413--18456 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
18403 ATATGCTTAT
*
18413 CTTATTTATTTATTTTATTTA
1 CTTATTTATTTA-TTTATCTA
18434 CTTATTTATTTATTTATCTA
1 CTTATTTATTTATTTATCTA
18454 CTT
1 CTT
18457 TTTTTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (20 bp):
CTTATTTATTTATTTATCTA
Done.