Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168498.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_95, 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: 90895
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
File 3 of 3
Found at i:85338 original size:4 final size:4
Alignment explanation
Indices: 85329--85361 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
85319 TATCAAATAT
85329 ATTA ATTA ATTA ATTA ATTA A-TA A-TA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
85362 GATTTTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 6 0.21
4 22 0.79
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:85673 original size:17 final size:17
Alignment explanation
Indices: 85629--85680 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
85619 TAAGCAAGAG
85629 TAATTCAATATT-ATTAT
1 TAATT-AATATTAATTAT
*
85646 TAATT-ATATTAATAAT
1 TAATTAATATTAATTAT
85662 TAATTAATATTAATTAT
1 TAATTAATATTAATTAT
85679 TA
1 TA
85681 TAAATATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 5 0.16
16 9 0.29
17 17 0.55
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATTAATATTAATTAT
Found at i:85677 original size:21 final size:22
Alignment explanation
Indices: 85648--85696 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
85638 ATTATTATTA
*
85648 ATTATATTAATAATTAAT-TAAT
1 ATTATATT-ATAATAAATATAAT
*
85670 ATTA-ATTATTATAAATATAAT
1 ATTATATTATAATAAATATAAT
85691 ATTATA
1 ATTATA
85697 ATGTTAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 7 0.30
21 11 0.48
22 5 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTATATTATAATAAATATAAT
Found at i:85698 original size:29 final size:27
Alignment explanation
Indices: 85635--85698 Score: 62
Period size: 26 Copynumber: 2.4 Consensus size: 27
85625 AGAGTAATTC
*
85635 AATATTAT--TATTAATTATATTAATA
1 AATATTATAATATTAATTATATAAATA
* *
85660 ATTAAT-TAATATTAATTATTATAAATA
1 AATATTATAATATTAATTA-TATAAATA
85687 TAATATTATAAT
1 -AATATTATAAT
85699 GTTAGTTACC
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
24 1 0.03
25 4 0.14
26 9 0.31
27 7 0.24
28 4 0.14
29 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
AATATTATAATATTAATTATATAAATA
Found at i:85845 original size:22 final size:23
Alignment explanation
Indices: 85820--85871 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
85810 TTATAATAAA
85820 TAATAATAT-AGTAAATA-ATTAT
1 TAATAATATGA-TAAATATATTAT
*
85842 TAATTA-ATGATAAATATATTAT
1 TAATAATATGATAAATATATTAT
85864 TAA-AATAT
1 TAATAATAT
85872 CATACTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
TAATAATATGATAAATATATTAT
Found at i:86579 original size:18 final size:18
Alignment explanation
Indices: 86537--86582 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
86527 TACTAATACC
86537 TTATTATA-ATTAGATTA
1 TTATTATATATTAGATTA
*
86554 TTAATATATATTAGATTA
1 TTATTATATATTAGATTA
86572 -TATT-TATATTA
1 TTATTATATATTA
86583 TAAATCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 7 0.27
17 10 0.38
18 9 0.35
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TTATTATATATTAGATTA
Found at i:88450 original size:24 final size:25
Alignment explanation
Indices: 88402--88455 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
88392 ATAAATTACT
*
88402 ATTAATAAATAATAATATTTATT-A
1 ATTAATAAATAATAATATTAATTAA
*
88426 ATTAATAAATAAT-TTATTAATTTAA
1 ATTAATAAATAATAATATTAA-TTAA
88451 ATTAA
1 ATTAA
88456 AATAGTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 5 0.19
24 15 0.58
25 6 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTAATAAATAATAATATTAATTAA
Found at i:88507 original size:33 final size:36
Alignment explanation
Indices: 88427--88511 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 36
88417 TATTTATTAA
*
88427 TTAATAAATAAT-TTATTAATTTAAATTAAAATAGTT
1 TTAATTAATAATATTA-TAATTTAAATTAAAATAGTT
* * *
88463 TTAATT-TTAATATTATAATTT-AATT-ATATTG-T
1 TTAATTAATAATATTATAATTTAAATTAAAATAGTT
88495 TTAATTAATAATATTAT
1 TTAATTAATAATATTAT
88512 TTAAATTACT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
32 7 0.17
33 13 0.31
34 4 0.10
35 10 0.24
36 8 0.19
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (36 bp):
TTAATTAATAATATTATAATTTAAATTAAAATAGTT
Found at i:88508 original size:17 final size:17
Alignment explanation
Indices: 88421--88515 Score: 56
Period size: 17 Copynumber: 5.6 Consensus size: 17
88411 TAATAATATT
* *
88421 TATTAATTAATAAATAA
1 TATTATTTAATTAATAA
88438 TTTATTAATTTAAATTAA-AA
1 --TATT-ATTT-AATTAATAA
* *
88458 TAGT-TTTAATT-TTAA
1 TATTATTTAATTAATAA
*
88473 TATTA--TAATTTAATTA
1 TATTATTTAA-TTAATAA
*
88489 TATTGTTTAATTAATAA
1 TATTATTTAATTAATAA
88506 TATTATTTAA
1 TATTATTTAA
88516 ATTACTTATT
Statistics
Matches: 58, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
14 3 0.05
15 11 0.19
16 9 0.16
17 15 0.26
18 6 0.10
19 4 0.07
20 5 0.09
21 5 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TATTATTTAATTAATAA
Found at i:88531 original size:33 final size:30
Alignment explanation
Indices: 88469--88546 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 30
88459 AGTTTTAATT
* *
88469 TTAATATTATAATTT-AATTATATTGTTTAA
1 TTAATAATAT-ATTTAAATTATATTATTTAA
88499 TTAATAATATTATTTAAATTACTTATTATTTAA
1 TTAATAATA-TATTTAAATTA--TATTATTTAA
*
88532 ATAA-AATA-ATTTAAA
1 TTAATAATATATTTAAA
88547 CAATTGTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
30 19 0.46
31 6 0.15
32 4 0.10
33 12 0.29
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (30 bp):
TTAATAATATATTTAAATTATATTATTTAA
Found at i:89197 original size:21 final size:19
Alignment explanation
Indices: 89147--89200 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
89137 TAATAATTAC
89147 TATTAATTATAAATATATTGT
1 TATTAATT-T-AATATATTGT
*
89168 T-TCAATTTAATATATTGAT
1 TATTAATTTAATATATTG-T
89187 ATATTAATTTAATA
1 -TATTAATTTAATA
89201 ATATATTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 9 0.32
19 2 0.07
20 6 0.21
21 11 0.39
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (19 bp):
TATTAATTTAATATATTGT
Found at i:89412 original size:22 final size:21
Alignment explanation
Indices: 89378--89422 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
89368 TTATTAAATA
* *
89378 AATAATAATATTAATTTAGTT
1 AATAATAAGATTAATTTAATT
*
89399 AATATATAAGATTACTTTAATT
1 AATA-ATAAGATTAATTTAATT
89421 AA
1 AA
89423 AAAAATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (21 bp):
AATAATAAGATTAATTTAATT
Found at i:89609 original size:29 final size:27
Alignment explanation
Indices: 89548--89628 Score: 69
Period size: 29 Copynumber: 2.9 Consensus size: 27
89538 TTGCAATAAT
*
89548 TTAATATTAAATATTTTATTATAAATA
1 TTAATATTAAATAATTTATTATAAATA
*
89575 TATAATCATTAAATAGATTTA-TATAATTA
1 T-TAAT-ATTAAATA-ATTTATTATAAATA
*
89604 CTTAATAAATAAAT-ATTTATT-TAAA
1 -TTAAT-ATTAAATAATTTATTATAAA
89629 GTTATATATA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
27 9 0.20
28 5 0.11
29 25 0.57
30 5 0.11
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (27 bp):
TTAATATTAAATAATTTATTATAAATA
Found at i:89751 original size:28 final size:30
Alignment explanation
Indices: 89702--89761 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
89692 TCATACATAA
*
89702 TAATTTATATAATTTAGATATAAAATTAAT
1 TAATATATATAATTTAGATATAAAATTAAT
* *
89732 TAATATATATAA-TTA-TTATAATATTAAT
1 TAATATATATAATTTAGATATAAAATTAAT
89760 TA
1 TA
89762 TTTAAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 13 0.48
29 3 0.11
30 11 0.41
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (30 bp):
TAATATATATAATTTAGATATAAAATTAAT
Found at i:89761 original size:15 final size:15
Alignment explanation
Indices: 89720--89799 Score: 64
Period size: 14 Copynumber: 5.6 Consensus size: 15
89710 ATAATTTAGA
* *
89720 TATAAAATTAATTAA
1 TATAATATTAATTAT
89735 TAT-ATA-TAATTAT
1 TATAATATTAATTAT
89748 TATAATATTAATTAT
1 TATAATATTAATTAT
*
89763 T-TAA-ATTTA-TACT
1 TATAATATTAATTA-T
*
89776 ATATAAAATT-ATTAT
1 -TATAATATTAATTAT
89791 TATAATATT
1 TATAATATT
89800 TTAAATTATA
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
12 2 0.04
13 14 0.26
14 17 0.31
15 16 0.30
16 5 0.09
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (15 bp):
TATAATATTAATTAT
Found at i:89794 original size:21 final size:21
Alignment explanation
Indices: 89769--89816 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
89759 TTATTTAAAT
* *
89769 TTATACTATATAAAATTATTA
1 TTATAATATATAAAATTATAA
* *
89790 TTATAATATTTTAAATTATAA
1 TTATAATATATAAAATTATAA
89811 TTATAA
1 TTATAA
89817 ACCTTTTGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TTATAATATATAAAATTATAA
Found at i:90028 original size:12 final size:12
Alignment explanation
Indices: 89991--90031 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
89981 CTTATAAAAA
*
89991 TTATATTAATAA
1 TTATATTAATAT
*
90003 TGATATTAATTAT
1 TTATATTAA-TAT
90016 TTATATTAATAT
1 TTATATTAATAT
90028 TTAT
1 TTAT
90032 TAACTTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
TTATATTAATAT
Found at i:90634 original size:16 final size:16
Alignment explanation
Indices: 90594--90635 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
90584 TTTATATTTA
90594 ATTAATAAT-TAAATT
1 ATTAATAATATAAATT
*
90609 ATT-ATAAATATCAATT
1 ATTAAT-AATATAAATT
90625 ATTAATAATAT
1 ATTAATAATAT
90636 TTTATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 2 0.09
15 6 0.26
16 13 0.57
17 2 0.09
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAATAATATAAATT
Done.