Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168194.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_430, 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: 27110
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Found at i:682 original size:9 final size:9
Alignment explanation
Indices: 666--703 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
656 AAAGTTAGGG
666 GAAAAAAAA
1 GAAAAAAAA
*
675 GCAAAAAAA
1 GAAAAAAAA
684 GTAAAAAAAA
1 G-AAAAAAAA
694 -AAAAAAAA
1 GAAAAAAAA
702 GA
1 GA
704 TTCACAGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 8 0.32
9 10 0.40
10 7 0.28
ACGTcount: A:0.84, C:0.03, G:0.11, T:0.03
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:2066 original size:13 final size:13
Alignment explanation
Indices: 2048--2072 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2038 ATGTCACAAA
2048 AAAAGAAAAGAAG
1 AAAAGAAAAGAAG
2061 AAAAGAAAAGAA
1 AAAAGAAAAGAA
2073 AAATGGTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAGAAG
Found at i:3635 original size:32 final size:32
Alignment explanation
Indices: 3567--3635 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
3557 AAGCCAATAT
* * * *
3567 TAGCTAGCACCAATGAAGTTGTAAGGTTAGTT
1 TAGCTAGCACCAATGAAATTGTAAGCTCAGTC
*
3599 TAGCTAGCATCAATCGAAATT-TAAGCTCAGTC
1 TAGCTAGCACCAAT-GAAATTGTAAGCTCAGTC
3631 TAGCT
1 TAGCT
3636 GACATATAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 26 0.84
33 5 0.16
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (32 bp):
TAGCTAGCACCAATGAAATTGTAAGCTCAGTC
Found at i:3994 original size:32 final size:32
Alignment explanation
Indices: 3909--4212 Score: 155
Period size: 32 Copynumber: 9.2 Consensus size: 32
3899 AAATTAAAAT
* * *
3909 TTTAAGCTCAGATTA-CTTGGTACTCAATGAAA
1 TTTAAGCCCAGATTATC-TGGCACCCAATGAAA
*
3941 GTTTAAGCCTAGATTATCTGGCACCCAATGAAA
1 -TTTAAGCCCAGATTATCTGGCACCCAATGAAA
* * *
3974 TTTAAGCCCA-ATTTAACTGGCACTCGATGAAAAAA
1 TTTAAGCCCAGA-TTATCTGGCACCCAATG---AAA
* * * *
4009 TTTAAACCCAGATTACCTAGCACTCAATGAAA
1 TTTAAGCCCAGATTATCTGGCACCCAATGAAA
* * * *
4041 TTTTAAGTCTAAATTATCTGGCACCAAATGAAA
1 -TTTAAGCCCAGATTATCTGGCACCCAATGAAA
***** ** *
4074 TTTAAAATTGGATTATCTGGCTTCTAATGAAA
1 TTTAAGCCCAGATTATCTGGCACCCAATGAAA
* * * * *
4106 TTTAAGCCTAGTTTAGCTAGCACTCAATGAAAAA
1 TTTAAGCCCAGATTATCTGGCACCCAATG--AAA
* * * *
4140 TTTAAAG-CCATATTACCTCGCACTCAATGAAA
1 TTT-AAGCCCAGATTATCTGGCACCCAATGAAA
* * * * *
4172 TTTTAGGCCTAAATTATCTAGCGCCCAATGAAA
1 -TTTAAGCCCAGATTATCTGGCACCCAATGAAA
4205 TTTAAGCC
1 TTTAAGCC
4213 TGATTTAGTT
Statistics
Matches: 207, Mismatches: 52, Indels: 25
0.73 0.18 0.09
Matches are distributed among these distances:
31 1 0.00
32 80 0.39
33 72 0.35
34 24 0.12
35 29 0.14
36 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.31
Consensus pattern (32 bp):
TTTAAGCCCAGATTATCTGGCACCCAATGAAA
Found at i:4032 original size:35 final size:35
Alignment explanation
Indices: 3971--4040 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
3961 GCACCCAATG
* * *
3971 AAATTTAAGCCCAATTTAACTGGCACTCGATGAAA
1 AAATTTAAACCCAATTTAACTAGCACTCAATGAAA
*
4006 AAATTTAAACCCAGA-TTACCTAGCACTCAATGAAA
1 AAATTTAAACCCA-ATTTAACTAGCACTCAATGAAA
4041 TTTTAAGTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.24
Consensus pattern (35 bp):
AAATTTAAACCCAATTTAACTAGCACTCAATGAAA
Found at i:4143 original size:34 final size:32
Alignment explanation
Indices: 4099--4219 Score: 95
Period size: 34 Copynumber: 3.7 Consensus size: 32
4089 TCTGGCTTCT
*
4099 AATG-AAATTTAAGCCTAGTTTAGCTAGCACTC
1 AATGAAAATTTAAGCCTA-TTTACCTAGCACTC
*
4131 AATGAAAAATTTAAAGCC-ATATTACCTCGCACTC
1 AATG-AAAATTT-AAGCCTAT-TTACCTAGCACTC
* * * * * *
4165 AATGAAATTTTAGGCCTAAATTATCTAGCGCCC
1 AATGAAAATTTAAGCCT-ATTTACCTAGCACTC
4198 AATG-AAATTTAAGCCTGATTTA
1 AATGAAAATTTAAGCCT-ATTTA
4220 GTTAGCTCTT
Statistics
Matches: 70, Mismatches: 13, Indels: 12
0.74 0.14 0.13
Matches are distributed among these distances:
32 22 0.31
33 20 0.29
34 23 0.33
35 5 0.07
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (32 bp):
AATGAAAATTTAAGCCTATTTACCTAGCACTC
Found at i:4188 original size:131 final size:132
Alignment explanation
Indices: 3952--4209 Score: 365
Period size: 131 Copynumber: 2.0 Consensus size: 132
3942 TTTAAGCCTA
* *
3952 GATTATCTGGCACCCAATGAAATTTAAGCCCAATTTAACTGGCACTCGATGAAAAAATTTAAACC
1 GATTATCTGGCACCCAATGAAATTTAAGCCCAATTTAACTAGCACTCAATGAAAAAATTTAAACC
* *
4017 CAGATTACCTAGCACTCAATGAAATTTTAAGTCTAAATTATCTGGCACCAAATGAAATTTAAAAT
66 CAGATTACCTAGCACTCAATGAAATTTTAAGCCTAAATTATCTAGCACCAAATGAAATTTAAAAT
4082 TG
131 TG
** * * * * *
4084 GATTATCTGGCTTCTAATGAAATTTAAGCCTAGTTTAGCTAGCACTCAATG-AAAAATTTAAAGC
1 GATTATCTGGCACCCAATGAAATTTAAGCCCAATTTAACTAGCACTCAATGAAAAAATTTAAACC
* * * * *
4148 CATATTACCTCGCACTCAATGAAATTTTAGGCCTAAATTATCTAGCGCCCAATGAAATTTAA
66 CAGATTACCTAGCACTCAATGAAATTTTAAGCCTAAATTATCTAGCACCAAATGAAATTTAA
4210 GCCTGATTTA
Statistics
Matches: 110, Mismatches: 16, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
131 67 0.61
132 43 0.39
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (132 bp):
GATTATCTGGCACCCAATGAAATTTAAGCCCAATTTAACTAGCACTCAATGAAAAAATTTAAACC
CAGATTACCTAGCACTCAATGAAATTTTAAGCCTAAATTATCTAGCACCAAATGAAATTTAAAAT
TG
Found at i:4350 original size:32 final size:31
Alignment explanation
Indices: 4309--4385 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 31
4299 AGTTGGCACT
*
4309 CAATGAAAATTTAAGCTCAACT-TAGCTGATATC
1 CAAT-AAAATTTAAG-TCAACTGTAGCTGACA-C
* * *
4342 CAATAAAATTTAAGTCTAGTGTAGTTGACAC
1 CAATAAAATTTAAGTCAACTGTAGCTGACAC
4373 CAATAAAATTTAA
1 CAATAAAATTTAA
4386 ACCTAGTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 18 0.46
32 17 0.44
33 4 0.10
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (31 bp):
CAATAAAATTTAAGTCAACTGTAGCTGACAC
Found at i:4615 original size:14 final size:14
Alignment explanation
Indices: 4574--4619 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
4564 CATCTTAAGA
*
4574 AAAAAATAAAAAAC
1 AAAAAATAAAAACC
4588 AAAAAA-AAATAACC
1 AAAAAATAAA-AACC
*
4602 AAAAAATAACAACC
1 AAAAAATAAAAACC
4616 AAAA
1 AAAA
4620 CCAAAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 3 0.11
14 23 0.82
15 2 0.07
ACGTcount: A:0.80, C:0.13, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAAAATAAAAACC
Found at i:4994 original size:15 final size:14
Alignment explanation
Indices: 4974--5019 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
4964 CGTTACATAT
4974 ATAAAAATAATAATA
1 ATAAAAATAA-AATA
4989 ATAAAAAGTAAAATA
1 ATAAAAA-TAAAATA
*
5004 TTAAAAATAAAA-A
1 ATAAAAATAAAATA
5017 ATA
1 ATA
5020 CGTATGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 3 0.11
14 5 0.18
15 17 0.61
16 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (14 bp):
ATAAAAATAAAATA
Found at i:5002 original size:21 final size:21
Alignment explanation
Indices: 4977--5016 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4967 TACATATATA
*
4977 AAAATAATAATAATAAAAAGT
1 AAAATAATAAAAATAAAAAGT
*
4998 AAAATATTAAAAATAAAAA
1 AAAATAATAAAAATAAAAA
5017 ATACGTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (21 bp):
AAAATAATAAAAATAAAAAGT
Found at i:5072 original size:42 final size:42
Alignment explanation
Indices: 4968--5077 Score: 97
Period size: 42 Copynumber: 2.7 Consensus size: 42
4958 GTTGGCCGTT
4968 ACATATATAAAA-ATA-ATAATAATAAAAAGTAAAATATTAAA
1 ACATAT-TAAAACATATATAATAATAAAAAGTAAAATATTAAA
** * * *
5009 A-ATAAAAAATACGTATGTAATAGATATAAAG--AAATATTTAAA
1 ACATATTAAA-ACATATATAATA-ATAAAAAGTAAAATA-TTAAA
5051 ACATATTAAAACATATATAATAA-AAAA
1 ACATATTAAAACATATATAATAATAAAA
5078 TAATATAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
39 3 0.06
40 7 0.13
41 9 0.17
42 21 0.40
43 13 0.25
ACGTcount: A:0.65, C:0.04, G:0.05, T:0.27
Consensus pattern (42 bp):
ACATATTAAAACATATATAATAATAAAAAGTAAAATATTAAA
Found at i:5088 original size:16 final size:18
Alignment explanation
Indices: 5058--5112 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
5048 AAAACATATT
*
5058 AAAACATATATAATAAAA
1 AAAATATATATAATAAAA
*
5076 AATA-ATATA-AATAAAA
1 AAAATATATATAATAAAA
5092 ATAAATATATATAATAAAA
1 A-AAATATATATAATAAAA
5111 AA
1 AA
5113 GTTTAACCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 8 0.25
17 7 0.22
18 9 0.28
19 8 0.25
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATATATATAATAAAA
Found at i:5097 original size:19 final size:19
Alignment explanation
Indices: 5063--5111 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 19
5053 ATATTAAAAC
*
5063 ATATATAATAAAAA-ATA-
1 ATATATAATAAAAATAAAT
5080 ATATA-AATAAAAATAAAT
1 ATATATAATAAAAATAAAT
5098 ATATATAATAAAAA
1 ATATATAATAAAAA
5112 AGTTTAACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 8 0.29
17 7 0.25
18 5 0.18
19 8 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
ATATATAATAAAAATAAAT
Found at i:6654 original size:3 final size:3
Alignment explanation
Indices: 6648--6672 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6638 ATAATAATAA
6648 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
6673 TCCACCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:7124 original size:7 final size:7
Alignment explanation
Indices: 7114--7138 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
7104 ATTTTTTAAA
7114 AAATAAT
1 AAATAAT
7121 AAATAAT
1 AAATAAT
7128 AAATAAT
1 AAATAAT
7135 AAAT
1 AAAT
7139 TAAGATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATAAT
Found at i:9787 original size:27 final size:28
Alignment explanation
Indices: 9731--9787 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
9721 ATATTTAAGA
* *
9731 AATTTTATTTCATTAAAAATTTTCATAT
1 AATTTTATTTCATTAAAAATATTCAAAT
*
9759 AATTTTATTT-TTTAAAAAATATT-AAAT
1 AATTTTATTTCATT-AAAAATATTCAAAT
9786 AA
1 AA
9788 AGAATAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (28 bp):
AATTTTATTTCATTAAAAATATTCAAAT
Found at i:11862 original size:19 final size:21
Alignment explanation
Indices: 11830--11875 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
11820 TTGAAAAAAA
*
11830 TAAAAATTTCAAAACTTT-TT
1 TAAAAAATTCAAAACTTTATT
*
11850 TAAAAAATT-AAAATTTTATT
1 TAAAAAATTCAAAACTTTATT
11870 TAAAAA
1 TAAAAA
11876 TAAACTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAAAATTCAAAACTTTATT
Found at i:11876 original size:19 final size:20
Alignment explanation
Indices: 11830--11876 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
11820 TTGAAAAAAA
11830 TAAAAATTTCAAAACTTTTTT
1 TAAAAA-TTCAAAACTTTTTT
*
11851 AAAAAATT-AAAA-TTTTATT
1 TAAAAATTCAAAACTTTT-TT
11870 TAAAAAT
1 TAAAAAT
11877 AAACTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.17
19 12 0.52
20 2 0.09
21 5 0.22
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAAAATTCAAAACTTTTTT
Found at i:23940 original size:15 final size:14
Alignment explanation
Indices: 23915--23945 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
23905 AAAGAAACCT
23915 GAAAAAGAAAAAGA
1 GAAAAAGAAAAAGA
23929 GAAAATAGAAAAAGA
1 GAAAA-AGAAAAAGA
23944 GA
1 GA
23946 TGAGAAAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (14 bp):
GAAAAAGAAAAAGA
Done.