Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168322.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_546, 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: 23462
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Found at i:690 original size:19 final size:19
Alignment explanation
Indices: 663--701 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
653 AAATAAAGTT
663 AGGGAAAAAAAAGTAAAAA
1 AGGGAAAAAAAAGTAAAAA
* *
682 AGGGTAAAAAAGGTAAAAA
1 AGGGAAAAAAAAGTAAAAA
701 A
1 A
702 AAATATTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (19 bp):
AGGGAAAAAAAAGTAAAAA
Found at i:2126 original size:12 final size:12
Alignment explanation
Indices: 2083--2119 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
2073 TCATTCATGT
* *
2083 TTCATTCATTCA
1 TTCATCCATTTA
2095 TTCATCCATTTA
1 TTCATCCATTTA
2107 TTCATCCATTTA
1 TTCATCCATTTA
2119 T
1 T
2120 GTATCCACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (12 bp):
TTCATCCATTTA
Found at i:3829 original size:19 final size:19
Alignment explanation
Indices: 3807--3846 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3797 GGGAAAATGG
*
3807 AAAAAGTGAAAAAAAAAGA
1 AAAAAGGGAAAAAAAAAGA
*
3826 AAAAAGGGAAAAAAAAGGA
1 AAAAAGGGAAAAAAAAAGA
3845 AA
1 AA
3847 GTTTTGAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (19 bp):
AAAAAGGGAAAAAAAAAGA
Found at i:4486 original size:12 final size:12
Alignment explanation
Indices: 4469--4502 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
4459 GCATGTTACA
4469 AAAAAAAAAGAG
1 AAAAAAAAAGAG
4481 AAAAAAAAAGAG
1 AAAAAAAAAGAG
4493 AAAAAGAAAA
1 AAAAA-AAAA
4503 ATGGTTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAG
Found at i:5069 original size:17 final size:18
Alignment explanation
Indices: 5023--5069 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
5013 AGGAAAAATG
5023 AAAGAA-AAAT-AAAGTA
1 AAAGAAGAAATGAAAGTA
5039 AAAGAAGAAA-GAAAGTA
1 AAAGAAGAAATGAAAGTA
*
5056 AAA-TAGAAATGAAA
1 AAAGAAGAAATGAAA
5070 TGAATGGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (18 bp):
AAAGAAGAAATGAAAGTA
Found at i:5923 original size:29 final size:29
Alignment explanation
Indices: 5866--5923 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
5856 ATTAGTAAAA
* * * *
5866 TTTTAAGCTCAGTTTAGCTAGCATATAAG
1 TTTTAAGCCCAATTTAACTAGCACATAAG
*
5895 TTTTAAGCCCAATTTAACTAGCACGTAAG
1 TTTTAAGCCCAATTTAACTAGCACATAAG
5924 CCCATATTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (29 bp):
TTTTAAGCCCAATTTAACTAGCACATAAG
Found at i:6084 original size:32 final size:32
Alignment explanation
Indices: 6003--6084 Score: 78
Period size: 32 Copynumber: 2.6 Consensus size: 32
5993 TTAGTTGGTA
* *
6003 TGTAAGCCAAGAT-TAGCTAGCACCAATGAAGT
1 TGTAAGCCCA-ATCTAGCTAGCACCAATGAAAT
* * * *
6035 TGTAAGGCCAGTTTAGCTAGCATCAATCGAAAT
1 TGTAAGCCCAATCTAGCTAGCACCAAT-GAAAT
6068 T-TAAGCCCAATCTAGCT
1 TGTAAGCCCAATCTAGCT
6085 GACATATAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
31 1 0.03
32 34 0.85
33 5 0.12
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (32 bp):
TGTAAGCCCAATCTAGCTAGCACCAATGAAAT
Found at i:6095 original size:86 final size:85
Alignment explanation
Indices: 5937--6095 Score: 201
Period size: 86 Copynumber: 1.9 Consensus size: 85
5927 ATATTAATTG
* * * * * * * **
5937 GCACCAATAAAGTTTTAAGCCAGTTTCGTTAGCATCAATCAAAATTTAAGCCTAGTTTAGTTGGT
1 GCACCAATAAAGTTGTAAGCCAGTTTAGCTAGCATCAATCAAAATTTAAGCCCAATCTAGCTGAC
*
6002 ATGTAAGCCAAGATTAGCTA
66 ATATAAGCCAAGATTAGCTA
* *
6022 GCACCAATGAAGTTGTAAGGCCAGTTTAGCTAGCATCAATCGAAATTTAAGCCCAATCTAGCTGA
1 GCACCAATAAAGTTGTAA-GCCAGTTTAGCTAGCATCAATCAAAATTTAAGCCCAATCTAGCTGA
6087 CATATAAGC
65 CATATAAGC
6096 TCAATGTTAG
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
85 16 0.26
86 45 0.74
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (85 bp):
GCACCAATAAAGTTGTAAGCCAGTTTAGCTAGCATCAATCAAAATTTAAGCCCAATCTAGCTGAC
ATATAAGCCAAGATTAGCTA
Found at i:6527 original size:33 final size:33
Alignment explanation
Indices: 6490--6560 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 33
6480 GCACTCAATA
**
6490 AAATTTTAAGTTTAAATTATCTGGCACCAAATG
1 AAATTTTAAAATTAAATTATCTGGCACCAAATG
** * *
6523 AAA-TTTAAAATTGGATTATCTGGCTCCCAATG
1 AAATTTTAAAATTAAATTATCTGGCACCAAATG
6555 AAATTT
1 AAATTT
6561 AAGCATAGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
32 26 0.84
33 5 0.16
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (33 bp):
AAATTTTAAAATTAAATTATCTGGCACCAAATG
Found at i:6657 original size:131 final size:132
Alignment explanation
Indices: 6385--6661 Score: 360
Period size: 131 Copynumber: 2.1 Consensus size: 132
6375 ACTTGGTACT
** *
6385 CAATGAAAGTTTAAGCTTAGATTATCTGGCACCCAATAAAATTTAAGCCCAGTTTAGCTAGCACT
1 CAATGAAA-TTTAAAATTAGATTATCTGGCACCCAATAAAATTTAAGCACAGTTTAGCTAGCACT
* ** *
6450 CGATGAAAAAATTTAAACCTAGATTACCTAGCACTCAATAAAATTTTAAGTTTAAATTATCTGGC
65 CGATGAAAAAATTTAAACCTAGATTACCTAGCACTCAACAAAATTTTAAGCCTAAATTATCTAGC
6515 ACC
130 ACC
* * * * * * *
6518 AAATGAAATTTAAAATTGGATTATCTGGCTCCCAATGAAATTTAAGCATAGTTTAGCTAGTATTC
1 CAATGAAATTTAAAATTAGATTATCTGGCACCCAATAAAATTTAAGCACAGTTTAGCTAGCACTC
* * * *
6583 GAT-CAAAAATTTAAAACC-ATATTACCTCGCACTCAACAAAATTTTAGGCCTAAATTATCTAGC
66 GATGAAAAAATTT-AAACCTAGATTACCTAGCACTCAACAAAATTTTAAGCCTAAATTATCTAGC
6646 ACC
130 ACC
6649 CAATGAAATTTAA
1 CAATGAAATTTAA
6662 GCTCGATTTA
Statistics
Matches: 124, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
131 61 0.49
132 56 0.45
133 7 0.06
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (132 bp):
CAATGAAATTTAAAATTAGATTATCTGGCACCCAATAAAATTTAAGCACAGTTTAGCTAGCACTC
GATGAAAAAATTTAAACCTAGATTACCTAGCACTCAACAAAATTTTAAGCCTAAATTATCTAGCA
CC
Found at i:7460 original size:16 final size:15
Alignment explanation
Indices: 7439--7485 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
7429 CATTACATAT
7439 ATAAAAAATAATAATA
1 ATAAAAAATAA-AATA
*
7455 ATAAAAAGTAAAAT-
1 ATAAAAAATAAAATA
*
7469 ATTAAAAATAAAA-A
1 ATAAAAAATAAAATA
7483 ATA
1 ATA
7486 CGTATATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 13 0.50
15 3 0.12
16 10 0.38
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (15 bp):
ATAAAAAATAAAATA
Found at i:7468 original size:21 final size:21
Alignment explanation
Indices: 7443--7482 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
7433 ACATATATAA
*
7443 AAAATAATAATAATAAAAAGT
1 AAAATAATAAAAATAAAAAGT
*
7464 AAAATATTAAAAATAAAAA
1 AAAATAATAAAAATAAAAA
7483 ATACGTATAT
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:7543 original size:15 final size:16
Alignment explanation
Indices: 7523--7559 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
7513 TAAAACATAT
7523 TAAAAACATAA-AT-AA
1 TAAAAA-ATAATATAAA
7538 TAAAAAATAATATAAA
1 TAAAAAATAATATAAA
7554 TAAAAA
1 TAAAAA
7560 TGAAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 8 0.40
16 8 0.40
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (16 bp):
TAAAAAATAATATAAA
Found at i:9623 original size:27 final size:28
Alignment explanation
Indices: 9567--9623 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
9557 ATATTTAAGA
* *
9567 AATTTTATTTTATTAAAAATTTTCATAT
1 AATTTTATTTTATTAAAAATATTCAGAT
9595 AATTTTATTTT-TTAAAAAATATT-AGAT
1 AATTTTATTTTATT-AAAAATATTCAGAT
9622 AA
1 AA
9624 AGAATAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (28 bp):
AATTTTATTTTATTAAAAATATTCAGAT
Found at i:11570 original size:21 final size:20
Alignment explanation
Indices: 11533--11571 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11523 ATAAAAACAG
* *
11533 AAAAAATCAAAGATCAAAAT
1 AAAAAAACAAACATCAAAAT
11553 AAAAAAACAAACATTCAAA
1 AAAAAAACAAACA-TCAAA
11572 TATTTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.72, C:0.13, G:0.03, T:0.13
Consensus pattern (20 bp):
AAAAAAACAAACATCAAAAT
Found at i:11693 original size:19 final size:21
Alignment explanation
Indices: 11661--11706 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
11651 TTGAAAAAAA
*
11661 TAAAAATTTCAAAACTTT-TT
1 TAAAAAATTCAAAACTTTATT
*
11681 TAAAAAATT-AAAATTTTATT
1 TAAAAAATTCAAAACTTTATT
11701 TAAAAA
1 TAAAAA
11707 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:11707 original size:19 final size:20
Alignment explanation
Indices: 11661--11707 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
11651 TTGAAAAAAA
11661 TAAAAATTTCAAAACTTTTTT
1 TAAAAA-TTCAAAACTTTTTT
*
11682 AAAAAATT-AAAA-TTTTATT
1 TAAAAATTCAAAACTTTT-TT
11701 TAAAAAT
1 TAAAAAT
11708 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:21410 original size:17 final size:17
Alignment explanation
Indices: 21390--21432 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
21380 TTGATTATGG
21390 TTATAATTTTTTTGTAT
1 TTATAATTTTTTTGTAT
21407 TTATAATTTTTTTGTAT
1 TTATAATTTTTTTGTAT
*
21424 TTGTAATTT
1 TTATAATTT
21433 CATTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (17 bp):
TTATAATTTTTTTGTAT
Done.