Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168056.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_306, 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: 36646
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.51
File 2 of 2
Found at i:26733 original size:27 final size:28
Alignment explanation
Indices: 26689--26747 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
26679 AGAAAGTAAA
* ** *
26689 AAAATGAAAATACTAAA-TATATAAAAT
1 AAAATCAAAATAAAAAATTATAAAAAAT
*
26716 AAAATCAAAATAAAAAATTTTAAAAAAT
1 AAAATCAAAATAAAAAATTATAAAAAAT
26744 AAAA
1 AAAA
26748 AGGGATGATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (28 bp):
AAAATCAAAATAAAAAATTATAAAAAAT
Found at i:26960 original size:19 final size:19
Alignment explanation
Indices: 26883--26962 Score: 54
Period size: 19 Copynumber: 4.2 Consensus size: 19
26873 AAGGAAGTGC
**
26883 AAAAAAAAATGGAAATTAG
1 AAAAAAAAATAAAAATTAG
* * * *
26902 AAATAAAAA-GAAATTTGTG
1 AAAAAAAAATAAAAATT-AG
* * **
26921 AAAAAAAGAGAAAAACAAG
1 AAAAAAAAATAAAAATTAG
26940 AAAAAAAAATAAAAATTAG
1 AAAAAAAAATAAAAATTAG
26959 AAAA
1 AAAA
26963 CCTACCAATT
Statistics
Matches: 44, Mismatches: 15, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
18 5 0.11
19 36 0.82
20 3 0.07
ACGTcount: A:0.72, C:0.01, G:0.12, T:0.14
Consensus pattern (19 bp):
AAAAAAAAATAAAAATTAG
Found at i:27127 original size:87 final size:90
Alignment explanation
Indices: 26979--27156 Score: 299
Period size: 87 Copynumber: 2.0 Consensus size: 90
26969 AATTTCTTCT
*
26979 TAACTTCTTTTTTCCTTCTGGTTATTTTATTGCCAAAATCTCATCTACTTTCATGTACATGTTAT
1 TAACTTCTTTTTTCCTTCTGGTTATTTTATTGCCAAAATCTCATCTACTTTCATGTACATGTTAC
*
27044 ACTCATT-TCTCTACTTGTGAAGTA
66 ACTCATTCTCTCTACTTATGAAGTA
27068 TAACTTCTTTTTTCCTTCTGGTTATTTT-TT-CCAAAATCTCATCTACTTTCATGTACATGTTAC
1 TAACTTCTTTTTTCCTTCTGGTTATTTTATTGCCAAAATCTCATCTACTTTCATGTACATGTTAC
* *
27131 ACTCATTCTTTTTACTTATGAAGTA
66 ACTCATTCTCTCTACTTATGAAGTA
27156 T
1 T
27157 GGCTTTTCAT
Statistics
Matches: 84, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
87 39 0.46
88 17 0.20
89 28 0.33
ACGTcount: A:0.22, C:0.20, G:0.08, T:0.49
Consensus pattern (90 bp):
TAACTTCTTTTTTCCTTCTGGTTATTTTATTGCCAAAATCTCATCTACTTTCATGTACATGTTAC
ACTCATTCTCTCTACTTATGAAGTA
Found at i:27857 original size:13 final size:13
Alignment explanation
Indices: 27841--27874 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
27831 TTTTAAAATC
27841 AATTTTAAATTTA
1 AATTTTAAATTTA
*
27854 AATTTAAAATTTA
1 AATTTTAAATTTA
*
27867 AAATTTAA
1 AATTTTAA
27875 CTTAATAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTTTAAATTTA
Found at i:27863 original size:7 final size:7
Alignment explanation
Indices: 27841--27874 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
27831 TTTTAAAATC
*
27841 AATTTTA
1 AATTTAA
27848 AATTT-A
1 AATTTAA
27854 AATTTAA
1 AATTTAA
27861 AATTTAA
1 AATTTAA
27868 AATTTAA
1 AATTTAA
27875 CTTAATAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
AATTTAA
Found at i:32236 original size:160 final size:162
Alignment explanation
Indices: 31950--32254 Score: 483
Period size: 160 Copynumber: 1.9 Consensus size: 162
31940 AATAAAACAT
*
31950 AAGTAATATAATCAGAAGCAACCAGTCTGATTTGATCCTTTCGTTCTCATTATACTGTAACAAGC
1 AAGTAATATAATCAGAAGCAACCAGTCTGATTTGATCCTTTCATTCTCATTATACTGTAACAAGC
* * * *
32015 AACCACCTTGAATTGATAGTTTCTGGTCTATCCCGCAGATCCTTTTTATCTCTCATTCTACTAGT
66 AACCACCTTGAATTGATACTTTCTGGTCTACCCCACAGATACTTTTTATCTCTCATTCTACTAGT
32080 TCCTTAATGGTTGAAAGTGTTTATAGAATGAC
131 TCCTTAATGGTTGAAAGTGTTTATAGAATGAC
* * *
32112 AAGTAATATAATCAGAAGCAACCAGTC-GA-TTGATCCTTTCATTCTCATTATCCTGTAAGAATC
1 AAGTAATATAATCAGAAGCAACCAGTCTGATTTGATCCTTTCATTCTCATTATACTGTAACAAGC
*
32175 AACCACCTTGAATTGATACTTTCTGGTCTACCGCCACAGA-ACTTTTTCT-TCTCATTTCTACTA
66 AACCACCTTGAATTGATACTTTCTGGTCTACC-CCACAGATACTTTTTATCTCTCA-TTCTACTA
32238 GTTCCTTAATGGTTGAA
129 GTTCCTTAATGGTTGAA
32255 GTTTTAACAT
Statistics
Matches: 132, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
159 5 0.04
160 92 0.70
161 8 0.06
162 27 0.20
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (162 bp):
AAGTAATATAATCAGAAGCAACCAGTCTGATTTGATCCTTTCATTCTCATTATACTGTAACAAGC
AACCACCTTGAATTGATACTTTCTGGTCTACCCCACAGATACTTTTTATCTCTCATTCTACTAGT
TCCTTAATGGTTGAAAGTGTTTATAGAATGAC
Done.