Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168220.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_454, 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: 26308
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2354 original size:21 final size:21
Alignment explanation
Indices: 2328--2373 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2318 TTATTAATAA
*
2328 AATAATTAAAATTTTAATTT-T
1 AATAATCAAAA-TTTAATTTCT
2349 AATAATCAAAATTTAATTTCT
1 AATAATCAAAATTTAATTTCT
2370 AATA
1 AATA
2374 TTTTGATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
AATAATCAAAATTTAATTTCT
Found at i:5010 original size:21 final size:21
Alignment explanation
Indices: 4944--5010 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
4934 CTTGCCATGC
*
4944 CAGCTTCTATCATTGTAACAG
1 CAGCTTCCATCATTGTAACAG
* **
4965 CAGCTT-CATTCCTTGCTGTTC--
1 CAGCTTCCA-TCATTG-T-AACAG
4986 CAGCTTCCATCATTGTAACAG
1 CAGCTTCCATCATTGTAACAG
5007 CAGC
1 CAGC
5011 ACATTTCATC
Statistics
Matches: 33, Mismatches: 7, Indels: 12
0.63 0.13 0.23
Matches are distributed among these distances:
19 1 0.03
20 2 0.06
21 26 0.79
22 3 0.09
23 1 0.03
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (21 bp):
CAGCTTCCATCATTGTAACAG
Found at i:5665 original size:14 final size:14
Alignment explanation
Indices: 5646--5675 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5636 ATGATGCTTA
5646 ATACAGGATTGTCT
1 ATACAGGATTGTCT
5660 ATACAGGATTGTCT
1 ATACAGGATTGTCT
5674 AT
1 AT
5676 GTTGTTGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (14 bp):
ATACAGGATTGTCT
Found at i:16962 original size:2 final size:2
Alignment explanation
Indices: 16955--16981 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16945 CTCCATCGGC
16955 AT 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 AT A
16982 GAGGACAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25042 original size:25 final size:25
Alignment explanation
Indices: 25000--25089 Score: 69
Period size: 25 Copynumber: 3.5 Consensus size: 25
24990 AATTCATATC
* *
25000 TTATATATATTATGTTAATAATAATA
1 TTATATATTTTA-ATTAATAATAATA
25026 TTAT-TATTTTAAATTAATTAA-AAT-
1 TTATATATTTT-AATTAA-TAATAATA
* *
25050 TAATATATTTTAATTAAAAATATATA
1 TTATATATTTTAATTAATAATA-ATA
25076 TTAATATATGTTTA
1 TT-ATATAT-TTTA
25090 TTGGAAATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
23 2 0.04
24 10 0.20
25 20 0.39
26 9 0.18
27 6 0.12
28 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TTATATATTTTAATTAATAATAATA
Found at i:25076 original size:19 final size:20
Alignment explanation
Indices: 25039--25077 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
25029 TTATTTTAAA
*
25039 TTAATTAAAATTAATATATT
1 TTAATTAAAAATAATATATT
25059 TTAATTAAAAAT-ATATATT
1 TTAATTAAAAATAATATATT
25078 AATATATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAATTAAAAATAATATATT
Done.