Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168201.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_437, 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: 26890
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:52 original size:28 final size:28
Alignment explanation
Indices: 2--61 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1 C
*** *
2 CATAGGAGCAAAACGATGTCGTTTTGAG
1 CATAGGAGCAAAACGACACCGTTTTAAG
*
30 CATAGGATCAAAACGACACCGTTTTAAG
1 CATAGGAGCAAAACGACACCGTTTTAAG
58 CATA
1 CATA
62 AAAGGATCTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (28 bp):
CATAGGAGCAAAACGACACCGTTTTAAG
Found at i:332 original size:18 final size:17
Alignment explanation
Indices: 287--333 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
277 AAAAAAATTT
* *
287 TTTTTTATATATTATTA
1 TTTTTTATATTTTAGTA
304 TTTTTGT-TATTTTGAGTA
1 TTTTT-TATATTTT-AGTA
322 TTTTTTATATTT
1 TTTTTTATATTT
334 ATGCATGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTTTTATATTTTAGTA
Found at i:709 original size:14 final size:14
Alignment explanation
Indices: 692--749 Score: 62
Period size: 15 Copynumber: 4.0 Consensus size: 14
682 AACACTAATT
692 CTTAAATCCAAACC
1 CTTAAATCCAAACC
*
706 CTTAAAATCTAAACC
1 CTT-AAATCCAAACC
* *
721 CCTAAACTTCAAACC
1 CTTAAA-TCCAAACC
*
736 CTTAAATCAAAACC
1 CTTAAATCCAAACC
750 GCAAACCTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
14 12 0.34
15 23 0.66
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (14 bp):
CTTAAATCCAAACC
Found at i:853 original size:22 final size:23
Alignment explanation
Indices: 837--886 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
827 ACCCTCTAAA
837 CCTTAAAA-TCAAACCCTAAAAC
1 CCTTAAAACTCAAACCCTAAAAC
*
859 CCTTAAAACTC-AACCC-AAAAT
1 CCTTAAAACTCAAACCCTAAAAC
880 CC-TAAAA
1 CCTTAAAA
887 TCTGAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 5 0.19
21 6 0.23
22 13 0.50
23 2 0.08
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (23 bp):
CCTTAAAACTCAAACCCTAAAAC
Found at i:4352 original size:3 final size:3
Alignment explanation
Indices: 4301--4330 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4291 TTATTAAAAT
4301 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4331 ATATTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4363 original size:21 final size:20
Alignment explanation
Indices: 4298--4365 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
4288 CTATTATTAA
*
4298 AATTAATAATAATAATAA-T
1 AATTAAAAATAATAATAATT
* *
4317 AA-TAATAATAATAAATATTT
1 AATTAAAAATAAT-AATAATT
**
4337 TTTTAAAAATAATAATTAATT
1 AATTAAAAATAATAA-TAATT
4358 AATTAAAA
1 AATTAAAA
4366 CAAAACAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
18 10 0.26
19 6 0.16
20 3 0.08
21 19 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTAAAAATAATAATAATT
Found at i:20270 original size:21 final size:21
Alignment explanation
Indices: 20246--20299 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
20236 TCATATATAT
20246 TATTATTAATTTTAACTTTAC
1 TATTATTAATTTTAACTTTAC
** *
20267 TATTA-TAATATTTATTTTTAT
1 TATTATTAAT-TTTAACTTTAC
*
20288 TATAATTAATTT
1 TATTATTAATTT
20300 ACTTTTAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 4 0.15
21 19 0.70
22 4 0.15
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTATTAATTTTAACTTTAC
Found at i:20305 original size:21 final size:21
Alignment explanation
Indices: 20243--20305 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 21
20233 CTTTCATATA
* *
20243 TATTATTATTAATTTTAACTTTAC
1 TATTATAATTAA-TTT-ACTTT-T
20267 TATTATAA-T-ATTTA-TTTT
1 TATTATAATTAATTTACTTTT
20285 TATTATAATTAATTTACTTTT
1 TATTATAATTAATTTACTTTT
20306 AATCTCGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 8 0.24
19 4 0.12
20 6 0.18
21 7 0.21
22 1 0.03
23 1 0.03
24 7 0.21
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTATAATTAATTTACTTTT
Found at i:21622 original size:2 final size:2
Alignment explanation
Indices: 21615--21645 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
21605 ATCTTATTAA
*
21615 AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21646 CAAGTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Done.