Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168242.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_474, 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: 25695
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Found at i:5878 original size:16 final size:16
Alignment explanation
Indices: 5857--5903 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
5847 TTAGGGTTTT
*
5857 GATTTTAGAGTTTGGA
1 GATTTTAGGGTTTGGA
5873 GATTTTAGGGTTTGGA
1 GATTTTAGGGTTTGGA
5889 GATTTTAGGGTTTGG
1 GATTTTAGGGTTTGG
5904 GGTTTTGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.19, C:0.00, G:0.36, T:0.45
Consensus pattern (16 bp):
GATTTTAGGGTTTGGA
Found at i:5907 original size:53 final size:50
Alignment explanation
Indices: 5844--5954 Score: 134
Period size: 53 Copynumber: 2.1 Consensus size: 50
5834 GGATATAGAA
* *
5844 GGTTTAGGGTTTTGATTTTAGAGTTTGGAGATTTTAGGG-TTTGGAGATTTTAG
1 GGTTTGGGGTTTTGATTTAAGAGTTT-G-GATTTTAGGGATTTGG-GATTTT-G
* *
5897 GGTTTGGGGTTTTGATTTAAGGGTTTGGATTTTAGGGATTTTGGATTTTG
1 GGTTTGGGGTTTTGATTTAAGAGTTTGGATTTTAGGGATTTGGGATTTTG
5947 GGATTTGG
1 GG-TTTGG
5955 ATTTTATGGG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
50 3 0.06
51 21 0.40
52 5 0.10
53 23 0.44
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (50 bp):
GGTTTGGGGTTTTGATTTAAGAGTTTGGATTTTAGGGATTTGGGATTTTG
Found at i:5941 original size:16 final size:16
Alignment explanation
Indices: 5920--6074 Score: 80
Period size: 16 Copynumber: 10.2 Consensus size: 16
5910 GATTTAAGGG
5920 TTTGGATTTTAGGGAT
1 TTTGGATTTTAGGGAT
5936 TTTGGATTTT-GGGA-
1 TTTGGATTTTAGGGAT
5950 TTTGGATTTTATGGG-T
1 TTTGGATTTTA-GGGAT
* * *
5966 TTCGAATTTTAGGG-G
1 TTTGGATTTTAGGGAT
* **
5981 TTTGGATTTAAAAGAT
1 TTTGGATTTTAGGGAT
*
5997 TTT--A---GAGGG--
1 TTTGGATTTTAGGGAT
* *
6006 TTTGGATTTAAGAGAT
1 TTTGGATTTTAGGGAT
**
6022 TTTGGATTTTTAGGGGG
1 TTTGGA-TTTTAGGGAT
* *
6039 TTTGGATTTAAGAGAT
1 TTTGGATTTTAGGGAT
*
6055 TTTGGATTTTTAGGGGT
1 TTTGGA-TTTTAGGGAT
6072 TTT
1 TTT
6075 AAAAACTTAG
Statistics
Matches: 101, Mismatches: 25, Indels: 25
0.67 0.17 0.17
Matches are distributed among these distances:
9 3 0.03
11 3 0.03
14 14 0.14
15 16 0.16
16 43 0.43
17 22 0.22
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.48
Consensus pattern (16 bp):
TTTGGATTTTAGGGAT
Found at i:5949 original size:15 final size:15
Alignment explanation
Indices: 5910--5989 Score: 85
Period size: 16 Copynumber: 5.3 Consensus size: 15
5900 TTGGGGTTTT
*
5910 GATTTAAGGG-TTTG
1 GATTTTAGGGATTTG
5924 GATTTTAGGGATTTTG
1 GATTTTAGGGA-TTTG
5940 GATTTT-GGGATTTG
1 GATTTTAGGGATTTG
5954 GATTTTATGGG-TTTCG
1 GATTTTA-GGGATTT-G
* *
5970 AATTTTAGGGGTTTG
1 GATTTTAGGGATTTG
5985 GATTT
1 GATTT
5990 AAAAGATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
14 19 0.33
15 15 0.26
16 23 0.40
ACGTcount: A:0.17, C:0.01, G:0.33, T:0.49
Consensus pattern (15 bp):
GATTTTAGGGATTTG
Found at i:6009 original size:25 final size:24
Alignment explanation
Indices: 5971--6024 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 24
5961 TGGGTTTCGA
5971 ATTTTAGGGGTTTGGATTTAAAAG
1 ATTTTAGGGGTTTGGATTTAAAAG
*
5995 ATTTTAGAGGGTTTGGATTTAAGAG
1 ATTTTAG-GGGTTTGGATTTAAAAG
6020 ATTTT
1 ATTTT
6025 GGATTTTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 7 0.25
25 21 0.75
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (24 bp):
ATTTTAGGGGTTTGGATTTAAAAG
Found at i:6034 original size:33 final size:32
Alignment explanation
Indices: 5996--6073 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 32
5986 ATTTAAAAGA
5996 TTTTAGAGGGTTTGGATTTAAGAGATTTTGGAT
1 TTTTAG-GGGTTTGGATTTAAGAGATTTTGGAT
6029 TTTTAGGGGGTTTGGATTTAAGAGATTTTGGAT
1 TTTTA-GGGGTTTGGATTTAAGAGATTTTGGAT
6062 TTTTAGGGGTTT
1 TTTTAGGGGTTT
6074 TAAAAACTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
32 7 0.16
33 36 0.82
34 1 0.02
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (32 bp):
TTTTAGGGGTTTGGATTTAAGAGATTTTGGAT
Found at i:6889 original size:3 final size:3
Alignment explanation
Indices: 6856--6918 Score: 53
Period size: 3 Copynumber: 22.3 Consensus size: 3
6846 TTTTGTTTTT
* *
6856 TTA TAA TTA TT- TTA TT- TTA -TA TTA -AA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** *
6900 TCG TTA TTA TTA ATA TTA T
1 TTA TTA TTA TTA TTA TTA T
6919 AGTGAAATAA
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
2 7 0.15
3 39 0.85
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:8988 original size:31 final size:28
Alignment explanation
Indices: 8953--9017 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
8943 GTCTTAGAAA
8953 AGAGAAAAAATATAAATAAAAATGAAAATTT
1 AGAGAAAAAATA-AAATAAAAA--AAAATTT
* * *
8984 AGAGAAACAATAAAATTACAAAAAATTT
1 AGAGAAAAAATAAAATAAAAAAAAATTT
9012 AGAGAA
1 AGAGAA
9018 GCTAACACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 13 0.42
30 7 0.23
31 11 0.35
ACGTcount: A:0.66, C:0.03, G:0.11, T:0.20
Consensus pattern (28 bp):
AGAGAAAAAATAAAATAAAAAAAAATTT
Found at i:10393 original size:30 final size:30
Alignment explanation
Indices: 10322--10398 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
10312 TTTTCGTCCA
* * *
10322 ATAAAGAGCTTAATTGAATGAAAACAGATGT
1 ATAAA-AGTTTAATTGAATGAAAAAAGATAT
* *
10353 ATAAAAGTTTAATTGAGTGAAAAAATATAT
1 ATAAAAGTTTAATTGAATGAAAAAAGATAT
* * *
10383 GTAAAGGTTTACTTGA
1 ATAAAAGTTTAATTGA
10399 TTTGAAATAG
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 33 0.87
31 5 0.13
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (30 bp):
ATAAAAGTTTAATTGAATGAAAAAAGATAT
Found at i:11188 original size:10 final size:11
Alignment explanation
Indices: 11159--11186 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
11149 TTAGAAAAGA
11159 AAAAAAATTAC
1 AAAAAAATTAC
11170 AAAAAAATTAC
1 AAAAAAATTAC
11181 AAAAAA
1 AAAAAA
11187 TTTAGAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAATTAC
Found at i:11571 original size:14 final size:16
Alignment explanation
Indices: 11552--11584 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
11542 AAAAGATTCC
11552 TTTTTGTT-TA-TTAT
1 TTTTTGTTATAGTTAT
11566 TTTTTGTTATAGTTAT
1 TTTTTGTTATAGTTAT
11582 TTT
1 TTT
11585 CTTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 2 0.12
16 7 0.41
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (16 bp):
TTTTTGTTATAGTTAT
Found at i:15780 original size:2 final size:2
Alignment explanation
Indices: 15773--15797 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15763 AAGCTTAGTG
15773 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
15798 GTAATTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23124 original size:35 final size:35
Alignment explanation
Indices: 23059--23129 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
23049 GATGGTACGA
* *
23059 TGAACAAAAACTACTATTCTCAACCGATGGCATGG
1 TGAACAAAAACCACTATTCTCAACCAATGGCATGG
* **
23094 TGAACAAAAACCACTATTCTTAATTAATGGCATGG
1 TGAACAAAAACCACTATTCTCAACCAATGGCATGG
23129 T
1 T
23130 TTGAAACCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (35 bp):
TGAACAAAAACCACTATTCTCAACCAATGGCATGG
Found at i:25511 original size:10 final size:12
Alignment explanation
Indices: 25487--25537 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 12
25477 AATTGTTTAC
25487 TTTTATATAATT
1 TTTTATATAATT
25499 TTTTAT-TAATT
1 TTTTATATAATT
*
25510 TTATATATTTAA-T
1 TT-T-TATATAATT
25523 TTTTATATATATT
1 TTTTATATA-ATT
25536 TT
1 TT
25538 AATTTTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
11 12 0.36
12 9 0.27
13 9 0.27
14 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTATATAATT
Found at i:25529 original size:13 final size:13
Alignment explanation
Indices: 25494--25530 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
25484 TACTTTTATA
25494 TAATTTTT-TA-T
1 TAATTTTTATATT
25505 TAATTTTATATATT
1 TAATTTT-TATATT
25519 TAATTTTTATAT
1 TAATTTTTATAT
25531 ATATTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 7 0.30
12 1 0.04
13 7 0.30
14 8 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TAATTTTTATATT
Found at i:25533 original size:19 final size:17
Alignment explanation
Indices: 25511--25551 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
25501 TTATTAATTT
25511 TATATA-TTTAATTTTTA
1 TATATATTTTAA-TTTTA
25528 TATATATTTTAATTTTA
1 TATATATTTTAATTTTA
25545 TATATAT
1 TATATAT
25552 GTGAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATATATTTTAATTTTA
Found at i:25546 original size:13 final size:15
Alignment explanation
Indices: 25504--25551 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 15
25494 TAATTTTTTA
25504 TTAA-TTTTATATAT
1 TTAATTTTTATATAT
25518 TTAATTTTTATATATATT
1 TTAA-TTTT-TATATA-T
25536 TTAATTTTATATATAT
1 TTAATTTT-TATATAT
25552 GTGAATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.13
16 4 0.13
17 17 0.57
18 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTAATTTTTATATAT
Found at i:25558 original size:17 final size:15
Alignment explanation
Indices: 25502--25551 Score: 66
Period size: 15 Copynumber: 3.2 Consensus size: 15
25492 TATAATTTTT
25502 TATTAATTTTATATA
1 TATTAATTTTATATA
25517 T-TTAATTTTTATATA
1 TATTAA-TTTTATATA
25532 TATTTTAATTTTATATA
1 TA--TTAATTTTATATA
25549 TAT
1 TAT
25552 GTGAATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.13
15 12 0.39
17 11 0.35
18 4 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTAATTTTATATA
Done.