Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168287.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_514, 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: 24349
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Found at i:374 original size:43 final size:43
Alignment explanation
Indices: 308--392 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
298 AGGACTTTAA
*
308 TTTAAAGTTATTTAGCCTCTGTATAGAGGAGCCTATTTCTTAG
1 TTTAAAGTTATTTAGCCTCTGTATAGAGGAACCTATTTCTTAG
* * *
351 TTTAAAGTTGTTTAGTCTTTGTATAGAGGAACCTATTTCTTA
1 TTTAAAGTTATTTAGCCTCTGTATAGAGGAACCTATTTCTTA
393 AATTGTTTGC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.45
Consensus pattern (43 bp):
TTTAAAGTTATTTAGCCTCTGTATAGAGGAACCTATTTCTTAG
Found at i:716 original size:18 final size:18
Alignment explanation
Indices: 693--732 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
683 TATCAGGATT
693 TTAAATTG-GTATAGGGCC
1 TTAAATTGAGTATA-GGCC
*
711 TTAAATTGATTATAGGCC
1 TTAAATTGAGTATAGGCC
729 TTAA
1 TTAA
733 GCCTAGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (18 bp):
TTAAATTGAGTATAGGCC
Found at i:852 original size:134 final size:133
Alignment explanation
Indices: 641--881 Score: 342
Period size: 134 Copynumber: 1.8 Consensus size: 133
631 TCTAAAGCCT
* * * *
641 GTAATTGAACTTCGATTTGGATTTTCAGCTTTCGACGGTGTCTATCAGGATTTTAAATTGGTATA
1 GTAATTAAACTTCGATTTGGATTTTAAGCTTTCGACGGTGTCTATCAGCATTTTAAATTGATATA
706 GGGCCTTAAATTGATTATAGGCCTTAAGCCTAGTATAGGGTGTAGACACCCTATTTCGTCTGGGG
66 GGGCCTTAAATTGATTATAGGCCTTAAGCCTAGTATAGGGTGTAGACACCCTATTTCGTCTGGGG
771 CTA
131 CTA
* *
774 GTAATTAAACTTCGGTTTGGGTTTTTTAAGCTTTCGA-GGTGTCTATCAAGCA-TTTAAATTGAT
1 GTAATTAAACTTCGATTT-GG-ATTTTAAGCTTTCGACGGTGTCTATC-AGCATTTTAAATTGAT
* * * * *
837 ATGGGGCTTTAAATTGATTCTAGGCTTTAAGCCTAGTATGGGGTG
63 ATAGGGCCTTAAATTGATTATAGGCCTTAAGCCTAGTATAGGGTG
882 CCTTTTGATA
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
133 16 0.17
134 62 0.66
135 16 0.17
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (133 bp):
GTAATTAAACTTCGATTTGGATTTTAAGCTTTCGACGGTGTCTATCAGCATTTTAAATTGATATA
GGGCCTTAAATTGATTATAGGCCTTAAGCCTAGTATAGGGTGTAGACACCCTATTTCGTCTGGGG
CTA
Found at i:1820 original size:4 final size:4
Alignment explanation
Indices: 1806--1859 Score: 63
Period size: 4 Copynumber: 13.0 Consensus size: 4
1796 TTTTATATAC
* * *
1806 TTAT CTTAT TTAT TTGT TTAAT TTAC TTAT TTAT TTAT TTAT TCAT TTAT
1 TTAT -TTAT TTAT TTAT TT-AT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1856 TTAT
1 TTAT
1860 CTACTTGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
4 35 0.83
5 7 0.17
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:1835 original size:17 final size:16
Alignment explanation
Indices: 1815--1865 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
1805 CTTATCTTAT
*
1815 TTATTTGTTTAATTTAC
1 TTATTTATTT-ATTTAC
1832 TTATTTATTTATTTA-
1 TTATTTATTTATTTAC
*
1847 TTCATTTATTTATCTAC
1 TT-ATTTATTTATTTAC
1864 TT
1 TT
1866 GTTTTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 2 0.07
16 17 0.57
17 11 0.37
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.67
Consensus pattern (16 bp):
TTATTTATTTATTTAC
Found at i:5292 original size:29 final size:31
Alignment explanation
Indices: 5259--5333 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 31
5249 CTTATTTTTG
5259 AGTGATCAAATTTTAAAATTTT-AAA-ACTA
1 AGTGATCAAATTTTAAAATTTTAAAATACTA
* ** * *
5288 AGTGATCAAAATAGAAATTTTTAAAATATTA
1 AGTGATCAAATTTTAAAATTTTAAAATACTA
5319 AGTGATCAAACTTTT
1 AGTGATCAAA-TTTT
5334 TTTTTTAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
29 18 0.51
30 3 0.09
31 13 0.37
32 1 0.03
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (31 bp):
AGTGATCAAATTTTAAAATTTTAAAATACTA
Found at i:6422 original size:56 final size:55
Alignment explanation
Indices: 6273--6422 Score: 178
Period size: 56 Copynumber: 2.7 Consensus size: 55
6263 CTAATTATTC
* * * *
6273 CACCATTTTGGCTAAATTAGAAATATTTTTTCTTTTTCAAAATTTTTAAATTTTT
1 CACCATTTGGGCTAATTTAGAAATATTTTTTCTTTTTTAAAATTTTTAAAATTTT
* * *
6328 CACCATTTGGG-TCAATCTAGAAATATTTTCTTTTTTTTTTAAATTTTTAAAATTTT
1 CACCATTTGGGCT-AATTTAGAAATATTTT-TTCTTTTTTAAAATTTTTAAAATTTT
*
6384 CACCATTTGGGCTTATTTAGAAAT-TCTTTTTCCTTTTTT
1 CACCATTTGGGCTAATTTAGAAATAT-TTTTT-CTTTTTT
6423 CTATTTTCAA
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
54 1 0.01
55 27 0.34
56 51 0.64
57 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (55 bp):
CACCATTTGGGCTAATTTAGAAATATTTTTTCTTTTTTAAAATTTTTAAAATTTT
Found at i:7027 original size:12 final size:12
Alignment explanation
Indices: 7005--7046 Score: 68
Period size: 12 Copynumber: 3.5 Consensus size: 12
6995 TAATCATGCA
7005 AAAATACTAAA-
1 AAAATACTAAAT
7016 AAAATACATAAAT
1 AAAATAC-TAAAT
7029 AAAATACTAAAT
1 AAAATACTAAAT
7041 AAAATA
1 AAAATA
7047 AAAAAACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.24
12 15 0.52
13 7 0.24
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAATACTAAAT
Found at i:8280 original size:42 final size:41
Alignment explanation
Indices: 8235--8374 Score: 151
Period size: 42 Copynumber: 3.4 Consensus size: 41
8225 AGGCTCAACG
**
8235 ACTTTAAGAAAAATAAATGCTCTTCTAAACAGAGGCACCATG
1 ACTTTAA-AAAAATAAATGCTCTTCTAAACAGAGGCACCACA
* * *
8277 ACTTTGAAAAAATAAATTGCTCCTCTAAACAGAAGCACCACA
1 ACTTTAAAAAAATAAA-TGCTCTTCTAAACAGAGGCACCACA
** *
8319 ACTTT-GGAAAATAAAATGCTCATT-TAAATA-AGGCACCACA
1 ACTTTAAAAAAAT-AAATGCTC-TTCTAAACAGAGGCACCACA
8359 ACTTTAAAAAAATAAA
1 ACTTTAAAAAAATAAA
8375 ATACTCTTTG
Statistics
Matches: 82, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
40 17 0.21
41 29 0.35
42 36 0.44
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.24
Consensus pattern (41 bp):
ACTTTAAAAAAATAAATGCTCTTCTAAACAGAGGCACCACA
Found at i:8363 original size:40 final size:41
Alignment explanation
Indices: 8243--8383 Score: 153
Period size: 41 Copynumber: 3.4 Consensus size: 41
8233 CGACTTTAAG
**
8243 AAAAAT-AAATGCTCTTCTAAACAGAGGCACCATGACTTTGA
1 AAAAATAAAATGCTCTT-TAAACAGAGGCACCACAACTTTGA
* * *
8284 AAAAATAAATTGCTCCTCTAAACAGAAGCACCACAACTTTG-
1 AAAAATAAAATGCT-CTTTAAACAGAGGCACCACAACTTTGA
* * *
8325 GAAAATAAAATGCTCATTTAAATA-AGGCACCACAACTTTAA
1 AAAAATAAAATGCTC-TTTAAACAGAGGCACCACAACTTTGA
*
8366 AAAAATAAAATACTCTTT
1 AAAAATAAAATGCTCTTT
8384 GACAATCATG
Statistics
Matches: 83, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
40 18 0.22
41 37 0.45
42 26 0.31
43 2 0.02
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.25
Consensus pattern (41 bp):
AAAAATAAAATGCTCTTTAAACAGAGGCACCACAACTTTGA
Found at i:9331 original size:63 final size:63
Alignment explanation
Indices: 9275--9393 Score: 166
Period size: 63 Copynumber: 1.9 Consensus size: 63
9265 TTTGTCCTTT
* * *
9275 ATCACTGGGTCACTACTCATAGGTTTCTCAGTACTAGCCATTCCAAAACAAATTTTGTCACCC
1 ATCACTAGGTCACCACTCATAGGTTTCTCAATACTAGCCATTCCAAAACAAATTTTGTCACCC
* * * * *
9338 ATCACTAGGTCACCACTTATAGGTTTTTTAATACTAGCCATTTCAAAATAAATTTT
1 ATCACTAGGTCACCACTCATAGGTTTCTCAATACTAGCCATTCCAAAACAAATTTT
9394 ATCCATTGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 48 1.00
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (63 bp):
ATCACTAGGTCACCACTCATAGGTTTCTCAATACTAGCCATTCCAAAACAAATTTTGTCACCC
Found at i:13480 original size:46 final size:46
Alignment explanation
Indices: 13406--13495 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
13396 TCTTTTCAGA
* * *
13406 ATTTTTAAAATTTCCACCATTTGGGCTTATTTAGAAAATTTTTTTT
1 ATTTCTAAAATTTCCACCATCTGAGCTTATTTAGAAAATTTTTTTT
* *
13452 ATTTCTAAATTTTCTACCATCTGAGCTTATTTAGAAAATTTTTT
1 ATTTCTAAAATTTCCACCATCTGAGCTTATTTAGAAAATTTTTT
13496 CTTTTTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (46 bp):
ATTTCTAAAATTTCCACCATCTGAGCTTATTTAGAAAATTTTTTTT
Found at i:13845 original size:25 final size:25
Alignment explanation
Indices: 13799--13847 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
13789 TTCTCACCTA
*
13799 GAAATTTTATAAAAATTTATCATTT
1 GAAATTTTATAAAAATTCATCATTT
*
13824 GAAATTTT-TATAAATTCCATCATT
1 GAAATTTTATAAAAATT-CATCATT
13848 GGATAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (25 bp):
GAAATTTTATAAAAATTCATCATTT
Found at i:18670 original size:20 final size:20
Alignment explanation
Indices: 18645--18684 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
18635 TCAAAAAAAA
18645 AAATTACAAAATTTATTCAT
1 AAATTACAAAATTTATTCAT
*
18665 AAATTACAGAATTTATTCAT
1 AAATTACAAAATTTATTCAT
18685 TAGCAGCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (20 bp):
AAATTACAAAATTTATTCAT
Found at i:22717 original size:26 final size:26
Alignment explanation
Indices: 22680--22740 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
22670 GCATTATCTT
*
22680 ATAAGTAA-GGTTAAAATAGTGATAA
1 ATAATTAATGGTTAAAATAGTGATAA
*
22705 ATAATTAATGGTTAAAATATTGATAA
1 ATAATTAATGGTTAAAATAGTGATAA
22731 ATAAATTAAT
1 AT-AATTAAT
22741 AAACTCTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 7 0.22
26 18 0.56
27 7 0.22
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.34
Consensus pattern (26 bp):
ATAATTAATGGTTAAAATAGTGATAA
Done.