Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168005.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_260, 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: 41643
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:648 original size:12 final size:12
Alignment explanation
Indices: 633--680 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
623 GATATGGTAG
633 AAAATATTTTTT
1 AAAATATTTTTT
* **
645 AAAAAAAATTTT
1 AAAATATTTTTT
657 -AAATATTTTTT
1 AAAATATTTTTT
*
668 AGAATATTTTTT
1 AAAATATTTTTT
680 A
1 A
681 GATTCTTCTT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
AAAATATTTTTT
Found at i:1321 original size:109 final size:109
Alignment explanation
Indices: 1122--1322 Score: 235
Period size: 109 Copynumber: 1.8 Consensus size: 109
1112 ATACCAAATA
* * ** * *
1122 TAAGCACCAACCCAATATCATTATGTGAAAATTAAAACACCATCTATTAATCGAAGAGATTAGGC
1 TAAGCACCAACCCAAGATCATTATGTAAAAATTAAAACACCATCTATTAATAAAAAAGATTAGAC
* **
1187 ATATCGTTTAGGTAGTCATTGTGAATTCATGGAAGCAAAACATT
66 ATACCGTTTAGGTAGTCATCATGAATTCATGGAAGCAAAACATT
* * *
1231 TAAGCACTAACCCAAGATCATTATGTAAAAATTAGAACACC-TAC-GTTAATAAAAAAGATTAGA
1 TAAGCACCAACCCAAGATCATTATGTAAAAATTAAAACACCAT-CTATTAATAAAAAAGATTAGA
* * *
1294 TATACCTGTTTGGGTGGTCATCATGAATT
65 CATACC-GTTTAGGTAGTCATCATGAATT
1323 TGTGAAAACA
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
108 19 0.25
109 56 0.75
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (109 bp):
TAAGCACCAACCCAAGATCATTATGTAAAAATTAAAACACCATCTATTAATAAAAAAGATTAGAC
ATACCGTTTAGGTAGTCATCATGAATTCATGGAAGCAAAACATT
Found at i:3731 original size:15 final size:15
Alignment explanation
Indices: 3704--3743 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3694 TGCCAAAATT
*
3704 AAAATCAATATATAA
1 AAAATCAAAATATAA
* *
3719 AAAATTAAAATATCA
1 AAAATCAAAATATAA
3734 AAAATCAAAA
1 AAAATCAAAA
3744 GGAAAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATCAAAATATAA
Found at i:4563 original size:129 final size:129
Alignment explanation
Indices: 4376--4616 Score: 385
Period size: 129 Copynumber: 1.9 Consensus size: 129
4366 TAGTTTTATG
* * *
4376 AAAAATTGATATTTCAACTTTTTCTTTAGCATTTTTCAAATTTTATTTTATTTGATTTTTATTTA
1 AAAAATTGATATTTCAACTTTTTCCTTAGCATTTTTCAAATTTAATTTAATTTGATTTTTATTTA
4441 AAAGAACTTAGGAAAAATTGATATTCCAACTTTTTCCTAAATATTTTCAAAATTTATTCTAAAT
66 AAAGAACTTAGGAAAAATTGATATTCCAACTTTTTCCTAAATATTTTCAAAATTTATTCTAAAT
4505 AAAAATTGATATTTCAACTTTTTCCTTAGCATTTTTCAAAATTTAATTTAATTT-ATTTTTATTT
1 AAAAATTGATATTTCAACTTTTTCCTTAGCATTTTTC-AAATTTAATTTAATTTGATTTTTATTT
* * ** * *
4569 CAAAGAACTTAGGAAAATTTGATATTTTAACTTTTTCTTAAATTTTTT
65 AAAAGAACTTAGGAAAAATTGATATTCCAACTTTTTCCTAAATATTTT
4617 TTCATTTATT
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
129 88 0.86
130 14 0.14
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (129 bp):
AAAAATTGATATTTCAACTTTTTCCTTAGCATTTTTCAAATTTAATTTAATTTGATTTTTATTTA
AAAGAACTTAGGAAAAATTGATATTCCAACTTTTTCCTAAATATTTTCAAAATTTATTCTAAAT
Found at i:4723 original size:9 final size:8
Alignment explanation
Indices: 4707--4771 Score: 58
Period size: 9 Copynumber: 7.2 Consensus size: 8
4697 AAGTTCATAC
4707 AAAAATAA
1 AAAAATAA
4715 AATAAATAATA
1 AA-AAAT-A-A
4726 AAAAATGAA
1 AAAAAT-AA
4735 TAAAAATAA
1 -AAAAATAA
*
4744 TAAAAATAC
1 -AAAAATAA
4753 AAAAATATA
1 AAAAATA-A
4762 AAAAATAA
1 AAAAATAA
4770 AA
1 AA
4772 TATATGAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
8 12 0.24
9 22 0.45
10 12 0.24
11 3 0.06
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (8 bp):
AAAAATAA
Found at i:4739 original size:10 final size:9
Alignment explanation
Indices: 4707--4765 Score: 61
Period size: 8 Copynumber: 6.6 Consensus size: 9
4697 AAGTTCATAC
4707 AAAAATAA-
1 AAAAATAAT
4715 AATAAATAAT
1 AA-AAATAAT
4725 AAAAAATGAAT
1 -AAAAAT-AAT
4736 AAAAATAAT
1 AAAAATAAT
*
4745 AAAAAT-AC
1 AAAAATAAT
4753 AAAAAT-AT
1 AAAAATAAT
4761 AAAAA
1 AAAAA
4766 ATAAAATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
8 15 0.33
9 15 0.33
10 10 0.22
11 5 0.11
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.19
Consensus pattern (9 bp):
AAAAATAAT
Found at i:4766 original size:17 final size:16
Alignment explanation
Indices: 4707--4783 Score: 57
Period size: 19 Copynumber: 4.3 Consensus size: 16
4697 AAGTTCATAC
4707 AAAAATAAAATAAATAATA
1 AAAAAT-AAA-AAAT-ATA
4726 AAAAATGAATAAAA-ATAA
1 AAAAAT-AA-AAAATAT-A
4744 TAAAAATACAAAAATATA
1 -AAAAATA-AAAAATATA
*
4762 AAAAATAAAATATATGA
1 AAAAATAAAAAATAT-A
4779 AAAAA
1 AAAAA
4784 AATACTGCAA
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
16 7 0.14
17 15 0.30
18 7 0.14
19 20 0.40
20 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAAATAAAAAATATA
Found at i:4776 original size:16 final size:16
Alignment explanation
Indices: 4737--4783 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
4727 AAAATGAATA
4737 AAAATA-AT-AAAAAT
1 AAAATATATAAAAAAT
*
4751 ACAAAAATATAAAAAAT
1 A-AAATATATAAAAAAT
4768 AAAATATATGAAAAAA
1 AAAATATAT-AAAAAA
4784 AATACTGCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 1 0.04
15 4 0.15
16 9 0.33
17 13 0.48
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (16 bp):
AAAATATATAAAAAAT
Found at i:5286 original size:21 final size:19
Alignment explanation
Indices: 5246--5286 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
5236 ACCCAAATTT
*
5246 TGATGTCGAAAAATTCAAC
1 TGATGTCGAAAAATTAAAC
5265 TGATCGTCGAAAAATTTAAAC
1 TGAT-GTCGAAAAA-TTAAAC
5286 T
1 T
5287 TCTTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (19 bp):
TGATGTCGAAAAATTAAAC
Found at i:5880 original size:16 final size:17
Alignment explanation
Indices: 5859--5892 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5849 ATAGATCTTT
*
5859 GTTGCAAA-GTTTGGCA
1 GTTGCAAATGGTTGGCA
5875 GTTGCAAATGGTTGGCA
1 GTTGCAAATGGTTGGCA
5892 G
1 G
5893 CTTGACTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.24, C:0.12, G:0.35, T:0.29
Consensus pattern (17 bp):
GTTGCAAATGGTTGGCA
Found at i:6430 original size:15 final size:17
Alignment explanation
Indices: 6407--6439 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
6397 ATTTTCAAAC
6407 CTTTAAATTTTT-TGCT
1 CTTTAAATTTTTATGCT
6423 CTTT-AATTTTTATGCT
1 CTTTAAATTTTTATGCT
6439 C
1 C
6440 CTTGCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.18, C:0.15, G:0.06, T:0.61
Consensus pattern (17 bp):
CTTTAAATTTTTATGCT
Found at i:6604 original size:15 final size:15
Alignment explanation
Indices: 6584--6617 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6574 TAATTTTTTT
6584 ATTTCAAGCTCTTTA
1 ATTTCAAGCTCTTTA
* *
6599 ATTTCAATCTTTTTA
1 ATTTCAAGCTCTTTA
6614 ATTT
1 ATTT
6618 TTGTTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.03, T:0.56
Consensus pattern (15 bp):
ATTTCAAGCTCTTTA
Found at i:7746 original size:16 final size:16
Alignment explanation
Indices: 7727--7757 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7717 AAATTGTATG
*
7727 AACTTAATTATTCATT
1 AACTTAATCATTCATT
7743 AACTTAATCATTCAT
1 AACTTAATCATTCAT
7758 AAATCTATGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (16 bp):
AACTTAATCATTCATT
Found at i:19451 original size:22 final size:22
Alignment explanation
Indices: 19413--19457 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
19403 TTATGAAATT
19413 AGTTTCACAAAACTA-CCTTTA
1 AGTTTCACAAAACTACCCTTTA
19434 AGTTTCAACAAAGA-TACCCTTTA
1 AGTTTC-ACAAA-ACTACCCTTTA
19457 A
1 A
19458 ATATGAAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 6 0.29
22 7 0.33
23 8 0.38
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (22 bp):
AGTTTCACAAAACTACCCTTTA
Found at i:21619 original size:10 final size:10
Alignment explanation
Indices: 21601--21633 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
21591 GATAAATATA
21601 AATAA-TTTT
1 AATAATTTTT
21610 AATAATTTTT
1 AATAATTTTT
21620 AATAATTTGTT
1 AATAATTT-TT
21631 AAT
1 AAT
21634 TTTACAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 5 0.23
10 12 0.55
11 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (10 bp):
AATAATTTTT
Found at i:21683 original size:22 final size:20
Alignment explanation
Indices: 21658--21697 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
21648 ATACATAATA
21658 TAATTCAATTATACTATAATTT
1 TAATTCAA-TATACT-TAATTT
*
21680 TAATTTAATATACTTAAT
1 TAATTCAATATACTTAAT
21698 AATCTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 6 0.35
22 7 0.41
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATTCAATATACTTAATTT
Found at i:21815 original size:21 final size:21
Alignment explanation
Indices: 21758--21806 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
21748 ATTATTACCT
* * * *
21758 TTAATCTCATAATAATAATAT
1 TTAATTTCATCATTATAATAA
21779 TTAATTTCATCATTATAATAA
1 TTAATTTCATCATTATAATAA
21800 TTAATTT
1 TTAATTT
21807 TATTCTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAATTTCATCATTATAATAA
Found at i:29054 original size:14 final size:12
Alignment explanation
Indices: 29022--29047 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29012 TCGATTAAAA
29022 TTAAATTAATTT
1 TTAAATTAATTT
29034 TTAAATTAATTT
1 TTAAATTAATTT
29046 TT
1 TT
29048 TCAAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTAAATTAATTT
Found at i:30395 original size:10 final size:10
Alignment explanation
Indices: 30380--30434 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
30370 ATTTGACTAT
30380 TTTGATCAAG
1 TTTGATCAAG
*
30390 TTTGATCAAA
1 TTTGATCAAG
**
30400 TTTGA-CTTTG
1 TTTGATC-AAG
30410 TTTGATCAAG
1 TTTGATCAAG
*
30420 TTTGATAAAG
1 TTTGATCAAG
30430 TTTGA
1 TTTGA
30435 CTATGGGTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
9 1 0.03
10 34 0.94
11 1 0.03
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.45
Consensus pattern (10 bp):
TTTGATCAAG
Found at i:30416 original size:30 final size:29
Alignment explanation
Indices: 30351--30438 Score: 115
Period size: 30 Copynumber: 3.0 Consensus size: 29
30341 ATTTTAAAGA
* *
30351 TTGACTCAAGTTCGATCCAATTTGACTATT
1 TTGA-TCAAGTTTGATCAAATTTGACTATT
*
30381 TTGATCAAGTTTGATCAAATTTGACTTTGT
1 TTGATCAAGTTTGATCAAATTTGACTAT-T
30411 TTGATCAAGTTTGAT-AAAGTTTGACTAT
1 TTGATCAAGTTTGATCAAA-TTTGACTAT
30439 GGGTATTAGG
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.46
30 28 0.54
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.43
Consensus pattern (29 bp):
TTGATCAAGTTTGATCAAATTTGACTATT
Found at i:36341 original size:24 final size:24
Alignment explanation
Indices: 36310--36355 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
36300 TAAATGTTTT
*
36310 TCTTATG-CTTTTAATTTTCCAAG
1 TCTTATGCCATTTAATTTTCCAAG
*
36333 TCTTGATGCCATTTCATTTTCCA
1 TCTT-ATGCCATTTAATTTTCCA
36356 TTTTTCTAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 3 0.16
25 12 0.63
ACGTcount: A:0.20, C:0.22, G:0.09, T:0.50
Consensus pattern (24 bp):
TCTTATGCCATTTAATTTTCCAAG
Found at i:37561 original size:17 final size:17
Alignment explanation
Indices: 37500--37561 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
37490 TATCTTTAGG
37500 TTTTAA-AA-TTTTCA-
1 TTTTAATAACTTTTCAT
37514 TTTTAATAACTTTTC-T
1 TTTTAATAACTTTTCAT
**
37530 TATTTAGCAACTTTTCAT
1 T-TTTAATAACTTTTCAT
*
37548 TTTTAATAAGTTTT
1 TTTTAATAACTTTT
37562 AGATTTAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 6 0.16
15 2 0.05
16 6 0.16
17 22 0.58
18 2 0.05
ACGTcount: A:0.29, C:0.10, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTTAATAACTTTTCAT
Found at i:38971 original size:69 final size:67
Alignment explanation
Indices: 38887--39023 Score: 177
Period size: 69 Copynumber: 2.0 Consensus size: 67
38877 GATACAATAA
* * * *
38887 GATAGGATAAGATAATATTATGAATATGATTAAATTAAATAAT-GATATCTTATCTTATATTTGA
1 GATAGGATAAGATAATATTATAAATAGGATTAAATTAAACAATAG-CATC-T-TCTTATATTTGA
38951 TGTGT
63 TGTGT
* * *
38956 GATAGGATAATATAATATTATAAATAGGATTAGATTAAACAATAGCATCTTCTTATGTTTGATGT
1 GATAGGATAAGATAATATTATAAATAGGATTAAATTAAACAATAGCATCTTCTTATATTTGATGT
39021 GT
66 GT
39023 G
1 G
39024 CAAGGATTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
67 17 0.28
68 1 0.02
69 41 0.68
70 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.40
Consensus pattern (67 bp):
GATAGGATAAGATAATATTATAAATAGGATTAAATTAAACAATAGCATCTTCTTATATTTGATGT
GT
Found at i:40614 original size:14 final size:16
Alignment explanation
Indices: 40584--40620 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
40574 TTTTTATTTG
40584 ATATAAATTTATATGT
1 ATATAAATTTATATGT
40600 ATATAAA-TTAT-TGT
1 ATATAAATTTATATGT
*
40614 AAATAAA
1 ATATAAA
40621 AATATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 9 0.45
15 4 0.20
16 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (16 bp):
ATATAAATTTATATGT
Found at i:41426 original size:2 final size:2
Alignment explanation
Indices: 41419--41448 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41409 CTGTTTATGA
41419 AT AT AT AT 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
41449 TGAATTCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.