Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168452.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_663, 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: 20282
ACGTcount: A:0.65, C:0.05, G:0.12, T:0.18
Found at i:1357 original size:27 final size:23
Alignment explanation
Indices: 1312--1383 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 23
1302 AAATTTTTTA
** *
1312 AAAAATAAATTAAGAGAAAAAATT
1 AAAAATAAACAAAAAGAAAAAA-T
1336 AAATAA-AATACCAAAAAGGAAAAAAT
1 AAA-AATAA-A-CAAAAA-GAAAAAAT
1362 AAAAATAAACAAAAAGAAAAAA
1 AAAAATAAACAAAAAGAAAAAA
1384 GTAACAAAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
23 7 0.17
24 11 0.28
25 6 0.15
26 9 0.22
27 7 0.17
ACGTcount: A:0.76, C:0.04, G:0.07, T:0.12
Consensus pattern (23 bp):
AAAAATAAACAAAAAGAAAAAAT
Found at i:1366 original size:23 final size:22
Alignment explanation
Indices: 1336--1383 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
1326 AGAAAAAATT
*
1336 AAATAAAAT-ACCAAAAAGGAAA
1 AAATAAAATAAACAAAAA-GAAA
1358 AAATAAAAATAAACAAAAAGAAA
1 AAAT-AAAATAAACAAAAAGAAA
1381 AAA
1 AAA
1384 GTAACAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 12 0.52
24 7 0.30
ACGTcount: A:0.79, C:0.06, G:0.06, T:0.08
Consensus pattern (22 bp):
AAATAAAATAAACAAAAAGAAA
Found at i:3152 original size:8 final size:7
Alignment explanation
Indices: 3131--3219 Score: 58
Period size: 7 Copynumber: 12.4 Consensus size: 7
3121 ACAAAGAAAG
3131 AAAATAA
1 AAAATAA
3138 AAAATAA
1 AAAATAA
3145 AAAGAT--
1 AAA-ATAA
3151 AAAATAA
1 AAAATAA
* *
3158 AAGCACAA
1 AA-AATAA
*
3166 AAAAGAA
1 AAAATAA
3173 AAAATACA
1 AAAATA-A
3181 AAAATACA
1 AAAATA-A
*
3189 ACAA-AA
1 AAAATAA
*
3195 AATATAA
1 AAAATAA
*
3202 AAAGTAA
1 AAAATAA
3209 GAAAATAA
1 -AAAATAA
3217 AAA
1 AAA
3220 GGGACAAAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
5 2 0.03
6 6 0.09
7 31 0.48
8 25 0.39
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.11
Consensus pattern (7 bp):
AAAATAA
Found at i:3711 original size:23 final size:22
Alignment explanation
Indices: 3672--3719 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
3662 AGAAAAAATT
*
3672 AAATAAAATACCAAAAAAGGAAA
1 AAATAAAATAACAAAAAA-GAAA
3695 AAATAAAATAA-ACAAAAAGAAA
1 AAATAAAATAACA-AAAAAGAAA
3717 AAA
1 AAA
3720 GTAACAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.79, C:0.06, G:0.06, T:0.08
Consensus pattern (22 bp):
AAATAAAATAACAAAAAAGAAA
Found at i:3716 original size:22 final size:22
Alignment explanation
Indices: 3672--3719 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
3662 AGAAAAAATT
*
3672 AAATAAAATACCAAAAAAGGAAA
1 AAATAAAATA-CAAAAAAAGAAA
3695 AAATAAAATA-AACAAAAAGAAA
1 AAATAAAATACAA-AAAAAGAAA
3717 AAA
1 AAA
3720 GTAACAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 2 0.09
22 11 0.48
23 10 0.43
ACGTcount: A:0.79, C:0.06, G:0.06, T:0.08
Consensus pattern (22 bp):
AAATAAAATACAAAAAAAGAAA
Found at i:4389 original size:25 final size:26
Alignment explanation
Indices: 4338--4396 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
4328 GAAAGAAAAT
* * *
4338 AAAAAATAAAAAATAAATAAAGCACA
1 AAAAAAGAAAAAATAAACAAAACACA
*
4364 AAAAAAGAAAAAA-AAACAAAATACA
1 AAAAAAGAAAAAATAAACAAAACACA
4389 ACAAAAAG
1 A-AAAAAG
4397 TATAAAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 10 0.36
26 18 0.64
ACGTcount: A:0.80, C:0.08, G:0.05, T:0.07
Consensus pattern (26 bp):
AAAAAAGAAAAAATAAACAAAACACA
Found at i:4865 original size:12 final size:11
Alignment explanation
Indices: 4833--4867 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
4823 AAAAATTTTT
4833 TAAAATATAAA
1 TAAAATATAAA
4844 TAAAATATAAA
1 TAAAATATAAA
*
4855 TGAAAAAATAAA
1 T-AAAATATAAA
4867 T
1 T
4868 TAAGAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
TAAAATATAAA
Found at i:4867 original size:18 final size:18
Alignment explanation
Indices: 4841--4886 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 18
4831 TTTAAAATAT
4841 AAATAAAATATAA-ATGAAA
1 AAAT-AAATATAAGA-GAAA
4860 AAATAAAT-TAAGAGAAA
1 AAATAAATATAAGAGAAA
4877 AAATTAAATA
1 AAA-TAAATA
4887 AGATGCCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 10 0.42
18 10 0.42
19 4 0.17
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.22
Consensus pattern (18 bp):
AAATAAATATAAGAGAAA
Found at i:4878 original size:17 final size:17
Alignment explanation
Indices: 4856--4889 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4846 AAATATAAAT
4856 GAAAAAA-TAAATTAAGA
1 GAAAAAATTAAA-TAAGA
4873 GAAAAAATTAAATAAGA
1 GAAAAAATTAAATAAGA
4890 TGCCCAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (17 bp):
GAAAAAATTAAATAAGA
Found at i:4937 original size:17 final size:17
Alignment explanation
Indices: 4903--4955 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
4893 CCAAAAAGGA
*
4903 AAAAATAAAAAAAAAAC
1 AAAAAGAAAAAAAAAAC
**
4920 AAAAAGAAAAAAGTAAC
1 AAAAAGAAAAAAAAAAC
4937 AAAGTAAGAAAATAAAAAA
1 AAA--AAGAAAA-AAAAAA
4956 TTGGCGAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 17 0.61
19 7 0.25
20 4 0.14
ACGTcount: A:0.81, C:0.04, G:0.08, T:0.08
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAAC
Found at i:5540 original size:17 final size:16
Alignment explanation
Indices: 5510--5562 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
5500 ATAAACAAAG
5510 AAAGAAAAAAATAAAA
1 AAAGAAAAAAATAAAA
* *
5526 AAAGATAAAAGATAAAT
1 AAAGA-AAAAAATAAAA
*
5543 AAAGCACAAAAAAGAAAA
1 AAAG-A-AAAAAATAAAA
5561 AA
1 AA
5563 TACAAAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 5 0.17
17 13 0.45
18 11 0.38
ACGTcount: A:0.79, C:0.04, G:0.09, T:0.08
Consensus pattern (16 bp):
AAAGAAAAAAATAAAA
Found at i:6484 original size:21 final size:22
Alignment explanation
Indices: 6460--6516 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
6450 ATTTGAGAAA
*
6460 AAGAAGAAAAAAT-AAAAAATG
1 AAGAAGAAAAAATGAAAAAAAG
*
6481 AAGAGGCAAAAATATGAAAAAAAG
1 AAGAAG-AAAAA-ATGAAAAAAAG
*
6505 AAAAAGAAAAAA
1 AAGAAGAAAAAA
6517 ATTTATAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 5 0.17
22 6 0.21
23 7 0.24
24 11 0.38
ACGTcount: A:0.75, C:0.02, G:0.16, T:0.07
Consensus pattern (22 bp):
AAGAAGAAAAAATGAAAAAAAG
Found at i:9147 original size:29 final size:31
Alignment explanation
Indices: 9089--9150 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
9079 AACTATAAAG
9089 AAAGAAAGAAAAAAAATAAATAAAGCACAAAA
1 AAAGAAAGAAAAAAAATAAATAAA-CACAAAA
*
9121 AAAGAAA-AAAAAACAA-AAATACA-ACAAAA
1 AAAGAAAGAAAAAA-AATAAATAAACACAAAA
9150 A
1 A
9151 GTATAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 7 0.25
31 12 0.43
32 9 0.32
ACGTcount: A:0.81, C:0.08, G:0.06, T:0.05
Consensus pattern (31 bp):
AAAGAAAGAAAAAAAATAAATAAACACAAAA
Found at i:10279 original size:7 final size:7
Alignment explanation
Indices: 10269--10372 Score: 52
Period size: 7 Copynumber: 14.4 Consensus size: 7
10259 ACAAAGAAAG
10269 AAAATAA
1 AAAATAA
10276 AAAATAA
1 AAAATAA
*
10283 AAATAAAA
1 AAA-ATAA
10291 AAAGATAA
1 AAA-ATAA
*
10299 AAGATAA
1 AAAATAA
* *
10306 ATAA-AG
1 AAAATAA
* *
10312 CACA-AA
1 AAAATAA
*
10318 AAAAGAA
1 AAAATAA
10325 AAAATACA
1 AAAATA-A
10333 AAAATACA
1 AAAATA-A
10341 ACAAA-AA
1 A-AAATAA
*
10348 AATATAA
1 AAAATAA
*
10355 AAAGTAA
1 AAAATAA
10362 GAAAATAA
1 -AAAATAA
10370 AAA
1 AAA
10373 GGGACAAAAA
Statistics
Matches: 73, Mismatches: 18, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
6 7 0.10
7 35 0.48
8 28 0.38
9 3 0.04
ACGTcount: A:0.78, C:0.05, G:0.06, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:10306 original size:30 final size:28
Alignment explanation
Indices: 10270--10372 Score: 84
Period size: 28 Copynumber: 3.6 Consensus size: 28
10260 CAAAGAAAGA
* *
10270 AAATAAAAAATAAAAATAAAAAAAGATA
1 AAATAAAAAATAAAAACAAAAAAAGAAA
* * *
10298 AAA-GATAAATAAAGCACAAAAAAAGAAA
1 AAATAAAAAATAAA-AACAAAAAAAGAAA
* *
10326 AAATACAAAAAT-ACAACAAAAAAATATAA
1 AAATA-AAAAATAAAAACAAAAAAAGA-AA
10355 AAAGTAAGAAAATAAAAA
1 AAA-TAA-AAAATAAAAA
10373 GGGACAAAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
27 8 0.14
28 27 0.47
29 7 0.12
30 12 0.21
31 3 0.05
ACGTcount: A:0.78, C:0.05, G:0.06, T:0.12
Consensus pattern (28 bp):
AAATAAAAAATAAAAACAAAAAAAGAAA
Found at i:10311 original size:17 final size:17
Alignment explanation
Indices: 10265--10311 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
10255 ATAAACAAAG
*
10265 AAAGA-AAATAAAAAATA
1 AAAGATAAAT-AAAGATA
*
10282 AAA-ATAAAAAAAGATA
1 AAAGATAAATAAAGATA
10298 AAAGATAAATAAAG
1 AAAGATAAATAAAG
10312 CACAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.13
Consensus pattern (17 bp):
AAAGATAAATAAAGATA
Found at i:11541 original size:25 final size:24
Alignment explanation
Indices: 11491--11542 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
11481 ATAAAGAAAG
* *
11491 AAAGAAAAAAATAAATAAGCACAA
1 AAAGAAAAAAAAAAATAAACACAA
*
11515 AAAGAAAAAAACAAAATACA-ACAA
1 AAAGAAAAAAA-AAAATAAACACAA
11539 AAAG
1 AAAG
11543 TATAAAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.77, C:0.10, G:0.08, T:0.06
Consensus pattern (24 bp):
AAAGAAAAAAAAAAATAAACACAA
Found at i:13014 original size:29 final size:28
Alignment explanation
Indices: 12964--13019 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
12954 AGCAAGAAAA
* *
12964 GAATAAAAATGAAAAGTCAAAAGATTTG
1 GAATAAAAATGAAAAATCAAAAAATTTG
12992 GAATAAAAAATAGAAAAAT-AAAAAATTT
1 GAAT-AAAAAT-GAAAAATCAAAAAATTT
13020 TAAAACAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 14 0.58
30 6 0.25
ACGTcount: A:0.64, C:0.02, G:0.12, T:0.21
Consensus pattern (28 bp):
GAATAAAAATGAAAAATCAAAAAATTTG
Found at i:20253 original size:14 final size:14
Alignment explanation
Indices: 20217--20260 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
20207 AAAAAGCAAA
*
20217 AAATTAAAAAATTT
1 AAATTAAAAAAATT
* **
20231 TAAGGAAAAAAATT
1 AAATTAAAAAAATT
20245 AAATTAAAAAAATT
1 AAATTAAAAAAATT
20259 AA
1 AA
20261 GAAATAAATA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (14 bp):
AAATTAAAAAAATT
Done.