Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168390.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_607, 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: 21652
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Found at i:598 original size:3 final size:3
Alignment explanation
Indices: 592--646 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
582 TAAAAAAAGC
*
592 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
640 GTA ATA A
1 ATA ATA A
647 ATTTCATAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2482 original size:20 final size:20
Alignment explanation
Indices: 2445--2484 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2435 TTTTGTCACA
* * *
2445 TACTTGTTTGTTTGTTTATT
1 TACTTCTTTATTTATTTATT
2465 TACTTCTTTATTTATTTATT
1 TACTTCTTTATTTATTTATT
2485 AATTTTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (20 bp):
TACTTCTTTATTTATTTATT
Found at i:5657 original size:27 final size:27
Alignment explanation
Indices: 5619--5676 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
5609 TACCCATAAT
*
5619 GATAAACTCTTGATACACTATTTTTAA
1 GATAAACTCTTGATACACTATTTCTAA
5646 GATAAACTCTTGATACACTATTTCTAA
1 GATAAACTCTTGATACACTATTTCTAA
5673 GATA
1 GATA
5677 GTCTGACTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (27 bp):
GATAAACTCTTGATACACTATTTCTAA
Found at i:11692 original size:18 final size:18
Alignment explanation
Indices: 11669--11703 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11659 TATTATTATT
*
11669 AAATACGAAATACAAAAA
1 AAATACAAAATACAAAAA
*
11687 AAATACAAAATATAAAA
1 AAATACAAAATACAAAA
11704 TATCAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.14
Consensus pattern (18 bp):
AAATACAAAATACAAAAA
Found at i:11697 original size:25 final size:25
Alignment explanation
Indices: 11669--11762 Score: 99
Period size: 25 Copynumber: 3.9 Consensus size: 25
11659 TATTATTATT
*
11669 AAATACGAAATACAAAAAAAATACA
1 AAATACAAAATACAAAAAAAATACA
*
11694 AAATATAAAATATC-AAAAAAATACA
1 AAATACAAAATA-CAAAAAAAATACA
* *
11719 AAATATAAAATACCAAAAAAATA-A
1 AAATACAAAATACAAAAAAAATACA
11743 ACAA-AC-AAA-ACAAAAAAAAT
1 A-AATACAAAATACAAAAAAAAT
11763 GAGGGATGGT
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
22 10 0.16
23 3 0.05
24 4 0.06
25 44 0.71
26 1 0.02
ACGTcount: A:0.74, C:0.11, G:0.01, T:0.14
Consensus pattern (25 bp):
AAATACAAAATACAAAAAAAATACA
Found at i:11714 original size:18 final size:17
Alignment explanation
Indices: 11693--11728 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
11683 AAAAAAATAC
*
11693 AAAATATAAAATATCAAA
1 AAAATACAAAATAT-AAA
11711 AAAATACAAAATATAAA
1 AAAATACAAAATATAAA
11728 A
1 A
11729 TACCAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (17 bp):
AAAATACAAAATATAAA
Found at i:11823 original size:24 final size:23
Alignment explanation
Indices: 11782--11827 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
11772 TAGTGCTGCT
11782 ACCATACCCTACCACCCATCCCTC
1 ACCATACCCTACCACCCA-CCCTC
* **
11806 ACCATGCCCTACTTCCCACCCT
1 ACCATACCCTACCACCCACCCT
11828 TCTGATCACC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.22, C:0.57, G:0.02, T:0.20
Consensus pattern (23 bp):
ACCATACCCTACCACCCACCCTC
Found at i:12734 original size:10 final size:10
Alignment explanation
Indices: 12719--12757 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
12709 TAAAAAAAAA
12719 TTTTTTTAAT
1 TTTTTTTAAT
12729 TTTTTTTAGAT
1 TTTTTTTA-AT
*
12740 TTTTTTAAAT
1 TTTTTTTAAT
12750 ATTTTTTT
1 -TTTTTTT
12758 GTTATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (10 bp):
TTTTTTTAAT
Found at i:12772 original size:20 final size:21
Alignment explanation
Indices: 12722--12772 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
12712 AAAAAAATTT
*
12722 TTTTAATT-TTTTTTAGATTT
1 TTTTAATTATTTTTTAGATTA
* *
12742 TTTTAAATATTTTTTTG-TTA
1 TTTTAATTATTTTTTAGATTA
12762 TTTTAATTATT
1 TTTTAATTATT
12773 ATTCTTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (21 bp):
TTTTAATTATTTTTTAGATTA
Found at i:12850 original size:7 final size:7
Alignment explanation
Indices: 12836--12865 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
12826 CTTGTTTTAT
12836 AATAATA
1 AATAATA
*
12843 ATTAATA
1 AATAATA
12850 AATAATA
1 AATAATA
12857 AATAATA
1 AATAATA
12864 AA
1 AA
12866 ATATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AATAATA
Done.