Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168420.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_634, 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: 20997
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:729 original size:18 final size:17
Alignment explanation
Indices: 706--739 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
696 TCTAATTAAT
706 TAAATATAAAAAAATAAC
1 TAAATA-AAAAAAATAAC
*
724 TAAATAAAAAGAATAA
1 TAAATAAAAAAAATAA
740 TACAACCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (17 bp):
TAAATAAAAAAAATAAC
Found at i:1165 original size:21 final size:19
Alignment explanation
Indices: 1134--1184 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
1124 TATATAATGT
* *
1134 ATATTTAAAAAATTAATAA
1 ATATATAAAAAATAAATAA
*
1153 ATTTATATAAAAAGTAAATAA
1 A--TATATAAAAAATAAATAA
1174 ATATATAAAAA
1 ATATATAAAAA
1185 TATTTTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 11 0.41
21 16 0.59
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
ATATATAAAAAATAAATAA
Found at i:1541 original size:14 final size:14
Alignment explanation
Indices: 1522--1549 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1512 GATTTTGATT
1522 TTATTTAAAATTTA
1 TTATTTAAAATTTA
1536 TTATTTAAAATTTA
1 TTATTTAAAATTTA
1550 GTTTGAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATTTAAAATTTA
Found at i:2415 original size:16 final size:14
Alignment explanation
Indices: 2394--2428 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
2384 AATATGCAGT
2394 AAAAAAAGCTAAAAGG
1 AAAAAAAG--AAAAGG
2410 AAAAAAAGAAAAGG
1 AAAAAAAGAAAAGG
2424 AAAAA
1 AAAAA
2429 GCAAGTGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
16 8 0.42
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (14 bp):
AAAAAAAGAAAAGG
Found at i:5361 original size:20 final size:20
Alignment explanation
Indices: 5319--5362 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5309 TATTTATAGA
* *
5319 TATTTAATAAATAAACTTTT
1 TATTAAATAAATAAACTTAT
5339 TATTAAATAATATAAA-TTAT
1 TATTAAATAA-ATAAACTTAT
5359 TATT
1 TATT
5363 TTAGATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TATTAAATAAATAAACTTAT
Found at i:5418 original size:27 final size:26
Alignment explanation
Indices: 5370--5440 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 26
5360 ATTTTAGATT
*
5370 AATTATAATTAATATATTTTTATTTAAAA
1 AATTAT-ATTAATATATATTTA--TAAAA
5399 AA-TATATTAATATATATTTATAAAA
1 AATTATATTAATATATATTTATAAAA
* *
5424 AATTATATAAATCTATA
1 AATTATATTAATATATA
5441 AGATAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
25 7 0.18
26 12 0.32
27 14 0.37
28 3 0.08
29 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
AATTATATTAATATATATTTATAAAA
Found at i:5615 original size:22 final size:21
Alignment explanation
Indices: 5577--5617 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5567 GAGTAAAGGA
* *
5577 ATAAATATAATATAAAAATTC
1 ATAAATAAAATAAAAAAATTC
5598 ATAAATAAAAATAAAAAAAT
1 ATAAAT-AAAATAAAAAAAT
5618 ATTTTATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
ATAAATAAAATAAAAAAATTC
Found at i:7544 original size:27 final size:26
Alignment explanation
Indices: 7506--7558 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
7496 ATAAGATGAC
7506 ATTATTTAATCTAATCTTATTCATAAT
1 ATTATTTAATCTAATCTTA-TCATAAT
*
7533 ATTATATT-ATCTTATCTTATCATAAT
1 ATTAT-TTAATCTAATCTTATCATAAT
7559 TTTGTATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 7 0.29
27 15 0.62
28 2 0.08
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTATTTAATCTAATCTTATCATAAT
Found at i:9442 original size:32 final size:32
Alignment explanation
Indices: 9399--9481 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
9389 TATTAATTTA
*
9399 TATATAATTTTTATTAAAATTTTAAATTATAT
1 TATATATTTTTTATTAAAATTTTAAATTATAT
* * *
9431 TATATATTTTTTCA-TATCATTTTTATATTATAT
1 TATATATTTTTT-ATTA-AAATTTTAAATTATAT
*
9464 TAT-TATATTTTATTAAAA
1 TATATATTTTTTATTAAAA
9482 ATTATTAGGT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
31 2 0.05
32 22 0.54
33 17 0.41
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (32 bp):
TATATATTTTTTATTAAAATTTTAAATTATAT
Done.