Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168017.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_271, 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: 40655
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:427 original size:4 final size:4
Alignment explanation
Indices: 418--442 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
408 GGTTAAAGAT
418 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
443 CTCAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:9051 original size:10 final size:9
Alignment explanation
Indices: 9035--9059 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
9025 TTTGGCCTAG
9035 CTTTTTTTT
1 CTTTTTTTT
9044 CTTTTTTTT
1 CTTTTTTTT
9053 CTTTTTT
1 CTTTTTT
9060 GCAGATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:14464 original size:15 final size:15
Alignment explanation
Indices: 14441--14470 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
14431 ATATCTCATA
14441 ATTAATTTTAATTTT
1 ATTAATTTTAATTTT
*
14456 ATTATTTTTAATTTT
1 ATTAATTTTAATTTT
14471 TTCAGAACCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTAATTTTAATTTT
Found at i:19588 original size:27 final size:27
Alignment explanation
Indices: 19550--19608 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
19540 ATGAAGAGAA
19550 ACATGCTATCACATGGAGTGCTAAAAG
1 ACATGCTATCACATGGAGTGCTAAAAG
19577 ACATGCTATCACATGGAGTGCTAAAAG
1 ACATGCTATCACATGGAGTGCTAAAAG
*
19604 TCATG
1 ACATG
19609 GACTATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.24
Consensus pattern (27 bp):
ACATGCTATCACATGGAGTGCTAAAAG
Found at i:28467 original size:19 final size:20
Alignment explanation
Indices: 28443--28484 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28433 CTCATATCTT
28443 GTATTA-TTAAAAAATAAAC
1 GTATTATTTAAAAAATAAAC
**
28462 GTATTATTTACTAAATAAAC
1 GTATTATTTAAAAAATAAAC
28482 GTA
1 GTA
28485 ATGTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (20 bp):
GTATTATTTAAAAAATAAAC
Found at i:38244 original size:30 final size:29
Alignment explanation
Indices: 38181--38254 Score: 72
Period size: 30 Copynumber: 2.7 Consensus size: 29
38171 AAAATATAAA
*
38181 ATATAATTTT-TTTA-TTTT-ATTAAATT
1 ATATAATTTTAATTATTTTTAATTAAATT
38207 -TAT--TTTTAATTATTTTTAATTTAAATT
1 ATATAATTTTAATTATTTTTAA-TTAAATT
38234 ATATAATTTTATATT-TTTTTA
1 ATATAATTTTA-ATTATTTTTA
38255 TACATATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
23 4 0.10
24 3 0.08
25 7 0.18
26 1 0.03
27 7 0.18
28 3 0.08
30 11 0.28
31 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
ATATAATTTTAATTATTTTTAATTAAATT
Done.