Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168288.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_515, 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: 24345
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Found at i:1167 original size:11 final size:10
Alignment explanation
Indices: 1153--1197 Score: 58
Period size: 9 Copynumber: 4.5 Consensus size: 10
1143 TTAGAGGGTG
1153 AAAAGAGAGAT
1 AAAA-AGAGAT
1164 -AAAAGAGAAT
1 AAAAAGAG-AT
1174 AAAAAGAGAT
1 AAAAAGAGAT
1184 AAAAA-AGAT
1 AAAAAGAGAT
1193 AAAAA
1 AAAAA
1198 TAAATAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 13 0.41
10 12 0.38
11 7 0.22
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (10 bp):
AAAAAGAGAT
Found at i:1183 original size:20 final size:19
Alignment explanation
Indices: 1153--1197 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1143 TTAGAGGGTG
*
1153 AAAAGAGAGATAAAAGAGAAT
1 AAAA-AGAGATAAAAAAG-AT
1174 AAAAAGAGATAAAAAAGAT
1 AAAAAGAGATAAAAAAGAT
1193 AAAAA
1 AAAAA
1198 TAAATAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.30
20 12 0.52
21 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (19 bp):
AAAAAGAGATAAAAAAGAT
Found at i:3522 original size:22 final size:22
Alignment explanation
Indices: 3497--3538 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
3487 TTGGTATATA
3497 CTATTAGATATATTTGAAATAC
1 CTATTAGATATATTTGAAATAC
3519 CTATTAGATATATTTGAAAT
1 CTATTAGATATATTTGAAAT
3539 CCTTCAATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (22 bp):
CTATTAGATATATTTGAAATAC
Found at i:8901 original size:27 final size:27
Alignment explanation
Indices: 8863--8919 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
8853 GGATCTAGGT
8863 ATTTAGTATTAAATGATGTTAGCCCAC
1 ATTTAGTATTAAATGATGTTAGCCCAC
* *
8890 ATTTAGTATTAAATGATGTTTGCCTAC
1 ATTTAGTATTAAATGATGTTAGCCCAC
8917 ATT
1 ATT
8920 CAATTAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (27 bp):
ATTTAGTATTAAATGATGTTAGCCCAC
Found at i:14141 original size:30 final size:30
Alignment explanation
Indices: 14100--14158 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
14090 GAGGATAGGA
*
14100 TAATAATCATTTTATATCATATTTGGTTTG
1 TAATAACCATTTTATATCATATTTGGTTTG
14130 TAATAACCATTTTATATCATATTTGGTTT
1 TAATAACCATTTTATATCATATTTGGTTT
14159 ATATCTAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (30 bp):
TAATAACCATTTTATATCATATTTGGTTTG
Found at i:15123 original size:11 final size:10
Alignment explanation
Indices: 15109--15153 Score: 58
Period size: 9 Copynumber: 4.5 Consensus size: 10
15099 TTAGAGGGTG
15109 AAAAGAGAGAT
1 AAAA-AGAGAT
15120 -AAAAGAGAAT
1 AAAAAGAG-AT
15130 AAAAAGAGAT
1 AAAAAGAGAT
15140 AAAAA-AGAT
1 AAAAAGAGAT
15149 AAAAA
1 AAAAA
15154 TAAATAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 13 0.41
10 12 0.38
11 7 0.22
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (10 bp):
AAAAAGAGAT
Found at i:15139 original size:20 final size:19
Alignment explanation
Indices: 15109--15153 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
15099 TTAGAGGGTG
*
15109 AAAAGAGAGATAAAAGAGAAT
1 AAAA-AGAGATAAAAAAG-AT
15130 AAAAAGAGATAAAAAAGAT
1 AAAAAGAGATAAAAAAGAT
15149 AAAAA
1 AAAAA
15154 TAAATAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.30
20 12 0.52
21 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (19 bp):
AAAAAGAGATAAAAAAGAT
Found at i:17695 original size:42 final size:42
Alignment explanation
Indices: 17609--17692 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
17599 TTGCTTCTTT
* * *
17609 ATATAAACACTATTATATGAGAAAGAAACGGTTCCGATTGAA
1 ATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAA
17651 ATATAAACACTATTATACGAGAAAG-AACAGTTCCAATTGAA
1 ATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAA
17692 A
1 A
17693 ATACTGTGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 15 0.38
42 24 0.62
ACGTcount: A:0.48, C:0.13, G:0.14, T:0.25
Consensus pattern (42 bp):
ATATAAACACTATTATACGAGAAAGAAACAGTTCCAATTGAA
Found at i:24172 original size:23 final size:24
Alignment explanation
Indices: 24110--24175 Score: 82
Period size: 23 Copynumber: 2.7 Consensus size: 24
24100 TTTTTCAATT
*
24110 TAAAATAAGAAATAATAAGAGTAAA
1 TAAAATAAGAAA-AATAACAGTAAA
24135 TAAAAATAA-ACAAAATAACA-TAAA
1 T-AAAATAAGA-AAAATAACAGTAAA
24159 TAAAATAAGAAAAATAA
1 TAAAATAAGAAAAATAA
24176 AGTCAAAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 14 0.38
24 6 0.16
25 8 0.22
26 9 0.24
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (24 bp):
TAAAATAAGAAAAATAACAGTAAA
Done.