Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168028.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_281, 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: 39093
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Found at i:5074 original size:28 final size:28
Alignment explanation
Indices: 5017--5077 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
5007 TTTAATTCAC
* *
5017 ATATATATAAAAATTAAAATATATATTT
1 ATATATATAAAAATTAAAATATAAAATT
*
5045 ATATTTATAAAAATTAAAA-ATAAAAATT
1 ATATATATAAAAATTAAAATAT-AAAATT
5073 ATATA
1 ATATA
5078 AAAGTAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 2 0.07
28 26 0.93
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
ATATATATAAAAATTAAAATATAAAATT
Found at i:7473 original size:35 final size:35
Alignment explanation
Indices: 7433--7503 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
7423 TTGGTTTCAA
* *
7433 ACCATGCCACCAATTAAGAATAGTGGTTTTTGTTC
1 ACCATGCCACCAATTAAGAATAGTAGTTTTTATTC
* ** *
7468 ACCATGCCATCGGTTGAGAATAGTAGTTTTTATTC
1 ACCATGCCACCAATTAAGAATAGTAGTTTTTATTC
7503 A
1 A
7504 TCGTACCATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (35 bp):
ACCATGCCACCAATTAAGAATAGTAGTTTTTATTC
Found at i:16028 original size:31 final size:31
Alignment explanation
Indices: 15993--16059 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
15983 CTCATTTCTG
15993 TTGGGGAACACCACAGCTT-TGATACCATTTA
1 TTGGGGAACACCACAG-TTCTGATACCATTTA
*
16024 TTGGGGAACACCACAGTTCTGATACCATTTG
1 TTGGGGAACACCACAGTTCTGATACCATTTA
16055 TTGGG
1 TTGGG
16060 CTAAAAGCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 2 0.06
31 32 0.94
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (31 bp):
TTGGGGAACACCACAGTTCTGATACCATTTA
Found at i:16630 original size:52 final size:52
Alignment explanation
Indices: 16544--16648 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 52
16534 TATAACCATA
* *
16544 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTACCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
* * * * *
16596 CAAACTTACCTATTAAGAATCCCTTTCCTTTTAGAATTTTTCTCTTGCAAGT
1 CAAACTTACCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
16648 C
1 C
16649 TTCTTGTCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.38
Consensus pattern (52 bp):
CAAACTTACCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:16704 original size:11 final size:11
Alignment explanation
Indices: 16673--16704 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
16663 GCAATATCTG
*
16673 ACAAATCTCAA
1 ACAAATCTCTA
16684 ACAAATCTCTA
1 ACAAATCTCTA
16695 ACAAATCTCT
1 ACAAATCTCT
16705 TATGAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (11 bp):
ACAAATCTCTA
Found at i:16975 original size:24 final size:24
Alignment explanation
Indices: 16948--17043 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 24
16938 CATGCACTTC
*
16948 TCACATCTCGAACTTTCAGCTCTT
1 TCACATCTCGAACCTTCAGCTCTT
*
16972 TCACATATCGAACCTTC-GCTCTT
1 TCACATCTCGAACCTTCAGCTCTT
* * *
16995 TCCACATCTTGAATCTTCAACTCTT
1 T-CACATCTCGAACCTTCAGCTCTT
** *
17020 CTCATGTTTCGAACCTTCAGCTCT
1 -TCACATCTCGAACCTTCAGCTCT
17044 GATACCACTT
Statistics
Matches: 57, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
23 7 0.12
24 28 0.49
25 21 0.37
26 1 0.02
ACGTcount: A:0.21, C:0.33, G:0.08, T:0.38
Consensus pattern (24 bp):
TCACATCTCGAACCTTCAGCTCTT
Found at i:17624 original size:52 final size:52
Alignment explanation
Indices: 17538--17642 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 52
17528 TATAACCATA
* *
17538 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTACCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
* * * *
17590 CAAACTTACCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
17642 C
1 C
17643 TTCTTGTCCA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.26, C:0.29, G:0.09, T:0.37
Consensus pattern (52 bp):
CAAACTTACCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:17698 original size:11 final size:11
Alignment explanation
Indices: 17667--17698 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
17657 GCAATATCTG
*
17667 ACAAATCTCAA
1 ACAAATCTCTA
17678 ACAAATCTCTA
1 ACAAATCTCTA
17689 ACAAATCTCT
1 ACAAATCTCT
17699 TATGAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (11 bp):
ACAAATCTCTA
Found at i:19495 original size:16 final size:14
Alignment explanation
Indices: 19458--19507 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
19448 AATTTGATTT
19458 AACAAAAAA-AA-A
1 AACAAAAAATAATA
*
19470 AA-AGAAAATAACTA
1 AACAAAAAATAA-TA
19484 TAACAAAAAATAATA
1 -AACAAAAAATAATA
19499 AACAAAAAA
1 AACAAAAAA
19508 GAATCTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
11 5 0.16
12 4 0.13
14 10 0.32
15 4 0.13
16 8 0.26
ACGTcount: A:0.80, C:0.08, G:0.02, T:0.10
Consensus pattern (14 bp):
AACAAAAAATAATA
Found at i:19505 original size:13 final size:16
Alignment explanation
Indices: 19474--19507 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
19464 AAAAAAAAAG
19474 AAAATAACTATAACAA
1 AAAATAACTATAACAA
19490 AAAATAA-TA-AACAA
1 AAAATAACTATAACAA
19504 AAAA
1 AAAA
19508 GAATCTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 2 0.11
16 7 0.39
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAATAACTATAACAA
Found at i:20535 original size:13 final size:14
Alignment explanation
Indices: 20511--20539 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20501 CTTCTCTAAA
20511 TTTTATGTAATTTT
1 TTTTATGTAATTTT
20525 TTTTATG-AATTTT
1 TTTTATGTAATTTT
20538 TT
1 TT
20540 AGGGATAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (14 bp):
TTTTATGTAATTTT
Found at i:20698 original size:30 final size:29
Alignment explanation
Indices: 20630--20716 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 29
20620 CTCTAAATCT
* *
20630 TCTA-TTTCAAATCAATTGAACCTTTGAATA
1 TCTATTTTC-AATCAATT-AAACTTTTAATA
* *
20660 TATTTTTTCAATCAATTAAACTTTTACATA
1 TCTATTTTCAATCAATTAAACTTTTA-ATA
*
20690 TCTATTTTCATTCAATTAAACTCTTTA
1 TCTATTTTCAATCAATTAAACT-TTTA
20717 TTGGATGAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
29 7 0.15
30 32 0.68
31 8 0.17
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.47
Consensus pattern (29 bp):
TCTATTTTCAATCAATTAAACTTTTAATA
Found at i:25410 original size:20 final size:20
Alignment explanation
Indices: 25373--25411 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25363 TTTTGTAGTT
* *
25373 TTTTTTTTTCTATATTTTCA
1 TTTTTATTTATATATTTTCA
*
25393 TTTTTATTTATATTTTTTC
1 TTTTTATTTATATATTTTC
25412 TCTTTTCTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTATTTATATATTTTCA
Found at i:29546 original size:170 final size:170
Alignment explanation
Indices: 29264--29610 Score: 547
Period size: 170 Copynumber: 2.0 Consensus size: 170
29254 AAAGTTTTTA
* *
29264 AAATGTTTATAATTTAAAATAAATTGAAAAAACGGGATAGATTTGATCAAATCATTTATAAATTT
1 AAATGTTCATAATTTAAAATAAATTGAAAAAACGGCATAGATTTGATCAAATCATTTATAAATTT
* * * *
29329 AAAAATAAAAAATAAAAGTTCACATCATCGCACAAAAAAAGCCAACAACAAAAACGTATTCATAA
66 AAAAATAAAAAATAAAAGTTCACATCATAGCAAAAAAAAAACCAACAACAAAAACGTAATCATAA
*
29394 TATATTAATTATTTTTAGTTTTGATATATTTATAAGATTC
131 TATATTAATTATTTTTAATTTTGATATATTTATAAGATTC
29434 AAATGTTCATAATTTAAAATAAATTGAAAAAA-GGTCATAGATTTGATCAAAT-AGTTTATAAAT
1 AAATGTTCATAATTTAAAATAAATTGAAAAAACGG-CATAGATTTGATCAAATCA-TTTATAAAT
* *
29497 TTAAAAATAAAAAATGAAAGTTCACTTCATAG-AAAAAAACAAACCAACAACAAAAACGTAATCA
64 TTAAAAATAAAAAATAAAAGTTCACATCATAGCAAAAAAA-AAACCAACAACAAAAACGTAATCA
*
29561 TAGTATATTAATTATTTTTAATTTTGATATATTTATAAGATTC
128 TAATATATTAATTATTTTTAATTTTGATATATTTATAAGATTC
29604 AACATGT
1 AA-ATGT
29611 GAGTATTTTT
Statistics
Matches: 163, Mismatches: 10, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
169 9 0.06
170 150 0.92
171 4 0.02
ACGTcount: A:0.49, C:0.09, G:0.08, T:0.33
Consensus pattern (170 bp):
AAATGTTCATAATTTAAAATAAATTGAAAAAACGGCATAGATTTGATCAAATCATTTATAAATTT
AAAAATAAAAAATAAAAGTTCACATCATAGCAAAAAAAAAACCAACAACAAAAACGTAATCATAA
TATATTAATTATTTTTAATTTTGATATATTTATAAGATTC
Found at i:29666 original size:21 final size:21
Alignment explanation
Indices: 29626--29667 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29616 TTTTTTTTTG
* * *
29626 TATTAAAAATAATTATAAATA
1 TATTAAAAACAATGAAAAATA
29647 TATTAAAAACAATGAAAAATA
1 TATTAAAAACAATGAAAAATA
29668 ACTTATCCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
TATTAAAAACAATGAAAAATA
Found at i:30174 original size:32 final size:33
Alignment explanation
Indices: 30122--30204 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
30112 TTTTTATAAA
*
30122 ATAAA-AATAATAATTGTATATG-AA-AATATAT
1 ATAAATAATAA-AATTTTATATGAAATAATATAT
*
30153 TTAAATATATAAAATTTTATATGAAATAATATAT
1 ATAAATA-ATAAAATTTTATATGAAATAATATAT
*
30187 ATAAATAATTAAATTTTA
1 ATAAATAATAAAATTTTA
30205 AAATTTGATA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
31 4 0.09
32 11 0.25
33 16 0.36
34 13 0.30
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (33 bp):
ATAAATAATAAAATTTTATATGAAATAATATAT
Found at i:34226 original size:52 final size:52
Alignment explanation
Indices: 34165--34269 Score: 149
Period size: 52 Copynumber: 2.0 Consensus size: 52
34155 TATAAGTATA
**
34165 CAAACTTGCCTATTAGA-AATCCCTTTCCTCTTAGAATTCTTCTTCTACAAGT
1 CAAACTTGCCTATTA-ATAATCAATTTCCTCTTAGAATTCTTCTTCTACAAGT
* * *
34217 CAAACTTGCCTATTAATAATCAATTTTCTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAATAATCAATTTCCTCTTAGAATTCTTCTTCTACAAGT
34269 C
1 C
34270 TTCTTGTCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 1 0.02
52 46 0.98
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.41
Consensus pattern (52 bp):
CAAACTTGCCTATTAATAATCAATTTCCTCTTAGAATTCTTCTTCTACAAGT
Found at i:35163 original size:52 final size:52
Alignment explanation
Indices: 35097--35196 Score: 141
Period size: 52 Copynumber: 1.9 Consensus size: 52
35087 AGTATAAAAG
* *
35097 CTTGCCTATTAAGAATC-CTTTTTCTCTTGAACTT-TTTCTTCTACAAGTCAAA
1 CTTGCCTATTAAGAATCTC-TTTTCTCTTAAAATTCTTT-TTCTACAAGTCAAA
*
35149 CTTGTCTATTAAGAATCTCTTTTCTCTTAAAATTCTTTTTCTACAAGT
1 CTTGCCTATTAAGAATCTCTTTTCTCTTAAAATTCTTTTTCTACAAGT
35197 TTTTTTGTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
52 39 0.91
53 4 0.09
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.47
Consensus pattern (52 bp):
CTTGCCTATTAAGAATCTCTTTTCTCTTAAAATTCTTTTTCTACAAGTCAAA
Found at i:35631 original size:17 final size:16
Alignment explanation
Indices: 35593--35635 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
35583 ACTTTCATAG
**
35593 ATTTTTATATAACTTC
1 ATTTTTATATAAAATC
35609 ATTTTTATATAAAATC
1 ATTTTTATATAAAATC
35625 ATGTTTTATAT
1 AT-TTTTATAT
35636 TTGAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (16 bp):
ATTTTTATATAAAATC
Done.