Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168356.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_577, 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: 22578
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Found at i:372 original size:8 final size:8
Alignment explanation
Indices: 348--383 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
338 ATAAATTAGT
*
348 AATAATAA
1 AATAATTA
*
356 AAAAATTA
1 AATAATTA
364 AATAATTA
1 AATAATTA
372 AATAATTA
1 AATAATTA
380 AATA
1 AATA
384 CATACTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
AATAATTA
Found at i:4161 original size:21 final size:20
Alignment explanation
Indices: 4128--4176 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
4118 TTGTAACAAT
*
4128 AACAAC-AAA-AATAATATC
1 AACAACTAAACAATAACATC
4146 AACAACATAAACAATAACATC
1 AACAAC-TAAACAATAACATC
*
4167 AATAACTAAA
1 AACAACTAAA
4177 ACCAAGGCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 6 0.23
20 7 0.27
21 13 0.50
ACGTcount: A:0.65, C:0.18, G:0.00, T:0.16
Consensus pattern (20 bp):
AACAACTAAACAATAACATC
Found at i:4178 original size:21 final size:20
Alignment explanation
Indices: 4124--4178 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
4114 GATCTTGTAA
* *
4124 CAATAACAACAAAAATAATAT
1 CAATAACAA-AACAATAACAT
*
4145 CAACAACATAAACAATAACAT
1 CAATAACA-AAACAATAACAT
4166 CAATAACTAAAAC
1 CAATAAC-AAAAC
4179 CAAGGCACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.64, C:0.20, G:0.00, T:0.16
Consensus pattern (20 bp):
CAATAACAAAACAATAACAT
Found at i:5434 original size:20 final size:22
Alignment explanation
Indices: 5405--5444 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
5395 ATTCTAGAAG
5405 AAAAACAAAT-TGA-AAAAAAA
1 AAAAACAAATCTGACAAAAAAA
*
5425 AAAAAGAAATCTGACAAAAA
1 AAAAACAAATCTGACAAAAA
5445 TATAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 3 0.18
22 5 0.29
ACGTcount: A:0.75, C:0.07, G:0.07, T:0.10
Consensus pattern (22 bp):
AAAAACAAATCTGACAAAAAAA
Found at i:5571 original size:11 final size:11
Alignment explanation
Indices: 5555--5579 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5545 CCCGCATCCA
5555 AATCAAATTTT
1 AATCAAATTTT
5566 AATCAAATTTT
1 AATCAAATTTT
5577 AAT
1 AAT
5580 TGTAATTGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (11 bp):
AATCAAATTTT
Found at i:7468 original size:13 final size:13
Alignment explanation
Indices: 7450--7474 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7440 TTCAATGATT
7450 TTTTAATTTTTAA
1 TTTTAATTTTTAA
7463 TTTTAATTTTTA
1 TTTTAATTTTTA
7475 TATATTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTAATTTTTAA
Found at i:7558 original size:9 final size:10
Alignment explanation
Indices: 7539--7584 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
7529 TTATTTTTAT
7539 TTTATAAAAA
1 TTTATAAAAA
7549 TTTA-AAAAA
1 TTTATAAAAA
*
7558 TATATAAAAA
1 TTTATAAAAA
*
7568 TTAATAAAAA
1 TTTATAAAAA
*
7578 TATATAA
1 TTTATAA
7585 TTTGGCTCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
TTTATAAAAA
Found at i:7567 original size:20 final size:20
Alignment explanation
Indices: 7541--7584 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
7531 ATTTTTATTT
*
7541 TATAAAAATTTA-AAAAATA
1 TATAAAAATTAATAAAAATA
7560 TATAAAAATTAATAAAAATA
1 TATAAAAATTAATAAAAATA
7580 TATAA
1 TATAA
7585 TTTGGCTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TATAAAAATTAATAAAAATA
Found at i:14642 original size:20 final size:20
Alignment explanation
Indices: 14617--14657 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
14607 CTTTAAATTT
*
14617 TTTAAAAT-TAGATTTAATAA
1 TTTAAAATATA-ATATAATAA
14637 TTTAAAATATAATATAATAA
1 TTTAAAATATAATATAATAA
14657 T
1 T
14658 ATGACAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TTTAAAATATAATATAATAA
Found at i:14805 original size:43 final size:41
Alignment explanation
Indices: 14707--14805 Score: 101
Period size: 43 Copynumber: 2.3 Consensus size: 41
14697 TACGATTTAA
* *
14707 AATTTTAATAATAAATTTAATAAAATTAAATATATATATATT
1 AATTTTAATATTAAATTTAATAAAA-TAAATATATAAATATT
* *
14749 AATTGTGACATATTAATTTTAATATAAA-AAATATATAAATATTT
1 AATT-TTA-ATATTAAATTTAATA-AAATAAATATATAAATA-TT
14793 GAATTTTAATATT
1 -AATTTTAATATT
14806 TTATATTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
42 4 0.09
43 19 0.40
44 17 0.36
45 7 0.15
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (41 bp):
AATTTTAATATTAAATTTAATAAAATAAATATATAAATATT
Found at i:16030 original size:21 final size:22
Alignment explanation
Indices: 16006--16058 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
15996 CTCAAAATTA
* *
16006 ATAAAATATTA-TTTTTTAAAT
1 ATAAAATAATACTTTTTAAAAT
16027 ATAAAATAATACTTTTTAAAAT
1 ATAAAATAATACTTTTTAAAAT
16049 ATAAATATAA
1 ATAAA-ATAA
16059 AAATATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 10 0.36
22 14 0.50
23 4 0.14
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATAAAATAATACTTTTTAAAAT
Found at i:16814 original size:14 final size:14
Alignment explanation
Indices: 16779--16817 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
16769 ATTAAAATTA
16779 AAAATATAATATAC
1 AAAATATAATATAC
*
16793 AAAA-ATAATTTAC
1 AAAATATAATATAC
16806 AAAATATAATAT
1 AAAATATAATAT
16818 TCTTAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATATAATATAC
Found at i:18679 original size:20 final size:21
Alignment explanation
Indices: 18648--18688 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
18638 TCATTATCAG
18648 ATATGTATATTC-GATAATACA
1 ATATGTATATTCAGAT-ATACA
18669 ATATG-ATATTCAGATATACA
1 ATATGTATATTCAGATATACA
18689 TTTTCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (21 bp):
ATATGTATATTCAGATATACA
Done.