Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168167.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_406, 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: 28391
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:805 original size:13 final size:13
Alignment explanation
Indices: 769--820 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
759 ATATATATAT
**
769 TATATTAATAAAA
1 TATATTAATTTAA
782 T-TATT-ATTTAA
1 TATATTAATTTAA
*
793 TATTTTAATTTAA
1 TATATTAATTTAA
*
806 AATATTAATTTAA
1 TATATTAATTTAA
819 TA
1 TA
821 AATATTATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 5 0.16
12 7 0.23
13 19 0.61
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATATTAATTTAA
Found at i:835 original size:14 final size:14
Alignment explanation
Indices: 760--842 Score: 64
Period size: 14 Copynumber: 5.9 Consensus size: 14
750 TATTTAATTA
*
760 TATATATATTATATT
1 TATAAATATTAT-TT
*
775 AATAAA-ATTATTAT
1 TATAAATATTATT-T
* *
789 T-TAATATTTTAATT
1 TATAA-ATATTATTT
803 TA-AAATATTAATTT
1 TATAAATATT-ATTT
*
817 AATAAATATTATTT
1 TATAAATATTATTT
831 TATAAATATTAT
1 TATAAATATTAT
843 ATTAAATTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
13 8 0.15
14 30 0.57
15 15 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATAAATATTATTT
Found at i:896 original size:73 final size:71
Alignment explanation
Indices: 760--898 Score: 167
Period size: 73 Copynumber: 1.9 Consensus size: 71
750 TATTTAATTA
* * * *
760 TATATATATTATATTAATAAAATTATTATTTAATATTTTAATTTAAAATATTAATTTAATAAATA
1 TATAAATATTATATTAATAAAATTATTAATTAATATTTGAATTGAAAATATTAATTTAATAAATA
825 TTATTT
66 TTATTT
*
831 TATAAATATTATATTAAATTAAAATTTTTAAATTAAT-TTTGAATTGAAACAGTA-TAATTT-AT
1 TATAAATATTATATT-AA-TAAAATTATT-AATTAATATTTGAATTGAAA-A-TATTAATTTAAT
893 AAATAT
61 AAATAT
899 ATGAGTCGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
71 14 0.24
72 2 0.03
73 27 0.47
74 13 0.22
75 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (71 bp):
TATAAATATTATATTAATAAAATTATTAATTAATATTTGAATTGAAAATATTAATTTAATAAATA
TTATTT
Found at i:3192 original size:27 final size:27
Alignment explanation
Indices: 3154--3214 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
3144 TTAATAGAGC
*
3154 AATTAAAATGCTGTTTGTCAACTTAAA
1 AATTAAAATGCTGTTTGTCAACTCAAA
3181 AATTAAAATGCTGTTTGTCAACTCAAA
1 AATTAAAATGCTGTTTGTCAACTCAAA
3208 AATTAAA
1 AATTAAA
3215 GTGCATGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.34
Consensus pattern (27 bp):
AATTAAAATGCTGTTTGTCAACTCAAA
Found at i:5292 original size:14 final size:14
Alignment explanation
Indices: 5270--5349 Score: 63
Period size: 14 Copynumber: 5.5 Consensus size: 14
5260 CATTTTCTTT
*
5270 AAACTCTAAAATCA
1 AAACCCTAAAATCA
5284 AAACCCT-AAATCTTA
1 AAACCCTAAAATC--A
*
5299 AGACCCTAAAATCA
1 AAACCCTAAAATCA
* *
5313 AATCCCTAAAATATCC
1 AAACCCT-AAA-ATCA
* *
5329 AGATCCTAAAATCA
1 AAACCCTAAAATCA
5343 AAACCCT
1 AAACCCT
5350 TCAAATCTTA
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
13 5 0.10
14 20 0.40
15 13 0.26
16 12 0.24
ACGTcount: A:0.49, C:0.28, G:0.03, T:0.21
Consensus pattern (14 bp):
AAACCCTAAAATCA
Found at i:5307 original size:29 final size:30
Alignment explanation
Indices: 5275--5360 Score: 102
Period size: 30 Copynumber: 2.9 Consensus size: 30
5265 TCTTTAAACT
5275 CTAAAATCAAAACCCT-AAATCTTAAGACC
1 CTAAAATCAAAACCCTAAAATCTTAAGACC
* * ** *
5304 CTAAAATCAAATCCCTAAAATATCCAGATC
1 CTAAAATCAAAACCCTAAAATCTTAAGACC
*
5334 CTAAAATCAAAACCCTTCAAATCTTAA
1 CTAAAATCAAAACCC-TAAAATCTTAA
5361 AATCAAAACT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
29 15 0.33
30 23 0.51
31 7 0.16
ACGTcount: A:0.48, C:0.27, G:0.02, T:0.23
Consensus pattern (30 bp):
CTAAAATCAAAACCCTAAAATCTTAAGACC
Found at i:8862 original size:45 final size:45
Alignment explanation
Indices: 8798--8889 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
8788 TACAGGTGTT
*
8798 CAAGCTTTATGATATTCCCAATCTTTTTAAGCACGTGATGCCACA
1 CAAGCTTTATGATATTCCCAATCTTTTTAAGCACATGATGCCACA
*
8843 CAAGCTTTGTGATATTCCCAATCTTTTTAAGCACATGATGCCACA
1 CAAGCTTTATGATATTCCCAATCTTTTTAAGCACATGATGCCACA
8888 CA
1 CA
8890 GGATTACCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (45 bp):
CAAGCTTTATGATATTCCCAATCTTTTTAAGCACATGATGCCACA
Found at i:10718 original size:38 final size:39
Alignment explanation
Indices: 10676--10750 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 39
10666 TTGAATAACA
10676 AAATA-TAAATATTAGT-AATAAATAATATT-TTATTTTTC
1 AAATATTAAATATTAGTGAAT--ATAATATTATTATTTTTC
* *
10714 AAATATTGAATATTATTGAATATAATATTATTATTTT
1 AAATATTAAATATTAGTGAATATAATATTATTATTTT
10751 AATAATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
38 13 0.41
39 16 0.50
40 3 0.09
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (39 bp):
AAATATTAAATATTAGTGAATATAATATTATTATTTTTC
Found at i:14402 original size:128 final size:128
Alignment explanation
Indices: 14174--14423 Score: 362
Period size: 128 Copynumber: 2.0 Consensus size: 128
14164 AATGGAGAAT
*
14174 TGACATGAAGAATATTGCATTGCTGCAGTTACTCTACTAATTGGTATTTTTGAATAAAGTGCTGG
1 TGACATGAAGAATATTGCATTGCTGCAGTTACTCTACTAATTGGTATTTTTGAAAAAAGTGCTGG
*
14239 TGCAAGGATAAAAGCAAAAGCTAGAATGGTGAAAAGATTATTATAGC-GAATTAGCTCCAGGTA
66 TGCAAGGATAAAAGCAAAAGCTAGAATGGTGAAAAGATTAGTATAGCAG-ATTAGCTCCAGGTA
* *
14302 TGACATGAAGATTATTGCATTGCTGCAGTTACTCTACTAA-TGGTATTTTTGAAAAACATTGCTG
1 TGACATGAAGAATATTGCATTGCTGCAGTTACTCTACTAATTGGTATTTTTGAAAAA-AGTGCTG
* * * * * *
14366 GTTCCAGGCTAGAAG-AAAACGCTTGAATTGTGAAAAGATTAGTATAGCAGATTAGCTC
65 GTGCAAGGATAAAAGCAAAA-GCTAGAATGGTGAAAAGATTAGTATAGCAGATTAGCTC
14424 TAGATATGCA
Statistics
Matches: 109, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
127 19 0.17
128 89 0.82
129 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (128 bp):
TGACATGAAGAATATTGCATTGCTGCAGTTACTCTACTAATTGGTATTTTTGAAAAAAGTGCTGG
TGCAAGGATAAAAGCAAAAGCTAGAATGGTGAAAAGATTAGTATAGCAGATTAGCTCCAGGTA
Found at i:16163 original size:21 final size:21
Alignment explanation
Indices: 16138--16185 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
16128 GAATACTAGT
16138 GAGAAATGAAAATGAAAGATG
1 GAGAAATGAAAATGAAAGATG
16159 GAGAAATGAAAATGAAAGATG
1 GAGAAATGAAAATGAAAGATG
*
16180 AAGAAA
1 GAGAAA
16186 CGTGTAGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.60, C:0.00, G:0.27, T:0.12
Consensus pattern (21 bp):
GAGAAATGAAAATGAAAGATG
Found at i:16734 original size:2 final size:2
Alignment explanation
Indices: 16727--16757 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16717 CAGCTAGAAC
16727 TA TA 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 TA TA T
16758 CAACTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17729 original size:16 final size:16
Alignment explanation
Indices: 17703--17737 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
17693 ATATAAAAAA
17703 TATATTATAAATTTTAT
1 TATATTATAAATTTT-T
17720 TATA-TATAAATTTTT
1 TATATTATAAATTTTT
17735 TAT
1 TAT
17738 CTAATATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 10 0.56
17 4 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATATTATAAATTTTT
Found at i:20347 original size:406 final size:404
Alignment explanation
Indices: 19583--20368 Score: 1245
Period size: 406 Copynumber: 1.9 Consensus size: 404
19573 CCTACACCAG
* *
19583 ACTTCGACTTGCCTTTATGTTTCAAATCCTGAAAGCTCGGGAGAACGAAGATTTTGCCAAAGCCG
1 ACTTCGACTTGCCTTTATGTTTCAAATCCTGAAAGCTCGGGAGAACAAAGATTTCGCCAAAGCCG
* *
19648 CTGAGCTCACTAATGCTCTCCGGTTCGTTTCCTTCATCATAGTTTTCTTTTCAAGTATTTCTCGT
66 CTGAGCTCACTAATGCTCTCCGGTTCGTTCCCTTCACCATAGTTTTCTTTTCAAGTATTTCTCGT
* * *
19713 TAAACCAACATAATCTAAAACCTTTAATGGCTTTGAAAATCTTCATTTTAAGGCAACCTCCATCC
131 CAAACCAACATAATCTAAAACCTTTAATGGCTTTGAAAATCTTCATTTTAAGACAACCTCCAGCC
* * ** *
19778 CCTTATATAATAACAGAGACAAAACAGGGGAGGAGAAATATGAAATTGAGGCCAATTTAAAAATC
196 CCATATATAATAACAGAGACAAAACAGGGGAGGAGAAATATGAAATTAAGGCCAAACTAAAAAGC
19843 TTCAATAATTATAAAAATAACCGGCCAAATTCCTCAATCTTTAATAGATCAGATTGAAAGATTAA
261 TTCAATAATTATAAAAATAACCGGCCAAATTCCTCAATCTTTAATAGATCAGATTGAAAGATTAA
* *
19908 CAGAAGAATTAAGAAGAAGATGAGTTATGTTTCCAAAATTTTTAATAATTTAAACGGGGCATCCA
326 CAGAAGAATTAAGAACAAGATGAGTTATGTTTCCAAAAATTTTAATAATTTAAACGGGGCATCCA
19973 ATCTAAAATTTAAT
391 ATCTAAAATTTAAT
* * **
19987 ACTTCTACTTGCCTTTATGTTTCAAATCCTGAAAGCTCGGGAGAGCAAAGATTTCGCCAAAGTGG
1 ACTTCGACTTGCCTTTATGTTTCAAATCCTGAAAGCTCGGGAGAACAAAGATTTCGCCAAAGCCG
* *
20052 TTGAGCTCACTCATGCTCTCCGGTTCGTTCCCTTCACCATAGTTTTCATTTT-AAGTATTTTCTC
66 CTGAGCTCACTAATGCTCTCCGGTTCGTTCCCTTCACCATAGTTTTC-TTTTCAAGTA-TTTCTC
20116 GTCAAACCAACATAATCTAAAACCTTTAATGGCTTTGAAAATCTTCATTTTAAGACAAACCTCCA
129 GTCAAACCAACATAATCTAAAACCTTTAATGGCTTTGAAAATCTTCATTTTAAGAC-AACCTCCA
** * *
20181 GCCTGATATATACTAACAGAGACGAAACAGGGGAGGAGAAATATGAAATTAAGGCCAAACTAAAA
193 GCCCCATATATAATAACAGAGACAAAACAGGGGAGGAGAAATATGAAATTAAGGCCAAACTAAAA
* * * *
20246 AGCTTCAATAATTATAAAATTAACTGGCCAAATTCCTCAATCTTTAATAGA-CTATATTGAATGA
258 AGCTTCAATAATTATAAAAATAACCGGCCAAATTCCTCAATCTTTAATAGATC-AGATTGAAAGA
*
20310 TTAACAGAAGAATTAAGAACAAGGTGAGCTT-TGTTTCCAAAAATTTTAATAATTTAAAC
322 TTAACAGAAGAATTAAGAACAAGATGAG-TTATGTTTCCAAAAATTTTAATAATTTAAAC
20369 TTCTACTCAT
Statistics
Matches: 348, Mismatches: 29, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
404 107 0.31
405 65 0.19
406 174 0.50
407 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.31
Consensus pattern (404 bp):
ACTTCGACTTGCCTTTATGTTTCAAATCCTGAAAGCTCGGGAGAACAAAGATTTCGCCAAAGCCG
CTGAGCTCACTAATGCTCTCCGGTTCGTTCCCTTCACCATAGTTTTCTTTTCAAGTATTTCTCGT
CAAACCAACATAATCTAAAACCTTTAATGGCTTTGAAAATCTTCATTTTAAGACAACCTCCAGCC
CCATATATAATAACAGAGACAAAACAGGGGAGGAGAAATATGAAATTAAGGCCAAACTAAAAAGC
TTCAATAATTATAAAAATAACCGGCCAAATTCCTCAATCTTTAATAGATCAGATTGAAAGATTAA
CAGAAGAATTAAGAACAAGATGAGTTATGTTTCCAAAAATTTTAATAATTTAAACGGGGCATCCA
ATCTAAAATTTAAT
Found at i:23704 original size:24 final size:25
Alignment explanation
Indices: 23670--23731 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 25
23660 TTTATGAATA
23670 ATAATTTATTTATAT-TCA-AATAATT
1 ATAA-TTATTTATATAT-ATAATAATT
23695 ATAATTATTTAT-TATATAATAATT
1 ATAATTATTTATATATATAATAATT
**
23719 ATTTTTATTTATA
1 ATAATTATTTATA
23732 AAAAATTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 2 0.06
24 26 0.81
25 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
ATAATTATTTATATATATAATAATT
Found at i:23738 original size:20 final size:20
Alignment explanation
Indices: 23702--23740 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
23692 ATTATAATTA
*
23702 TTTATTATATAATAATTATT
1 TTTATTATATAAAAATTATT
23722 TTTATT-TATAAAAAATTAT
1 TTTATTATAT-AAAAATTAT
23741 CTACCAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATTATATAAAAATTATT
Done.