Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168151.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_392, 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: 29208
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Found at i:621 original size:10 final size:11
Alignment explanation
Indices: 590--618 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
580 TTTGTTTTGA
590 TAAATTTAATT
1 TAAATTTAATT
601 T-AATTTAATT
1 TAAATTTAATT
611 TAAATTTA
1 TAAATTTA
619 TTTGATCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TAAATTTAATT
Found at i:2863 original size:33 final size:34
Alignment explanation
Indices: 2821--2890 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
2811 TTTTGGTGCC
* *
2821 TTGACTTTGTTT-CTTTTTTGGCGTATGAGCATA
1 TTGACTTTGTTTCCCTTTGTGGCGTATGAGCATA
*
2854 TTGACTTTGTTTCCCTTTGTGGCGTATGAGTATA
1 TTGACTTTGTTTCCCTTTGTGGCGTATGAGCATA
2888 TTG
1 TTG
2891 CCAGAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 12 0.36
34 21 0.64
ACGTcount: A:0.14, C:0.13, G:0.23, T:0.50
Consensus pattern (34 bp):
TTGACTTTGTTTCCCTTTGTGGCGTATGAGCATA
Found at i:3497 original size:36 final size:36
Alignment explanation
Indices: 3450--3528 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
3440 GTTTGATGAG
3450 GCTCCTGAGACATCCTCAAGCCGTAGTGGGGCGACT
1 GCTCCTGAGACATCCTCAAGCCGTAGTGGGGCGACT
* *
3486 GCTCCTGAGACATCCTCAAGCCGTGGTGGGGTGACT
1 GCTCCTGAGACATCCTCAAGCCGTAGTGGGGCGACT
3522 GCTCCTG
1 GCTCCTG
3529 GAGCCACACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.16, C:0.30, G:0.32, T:0.22
Consensus pattern (36 bp):
GCTCCTGAGACATCCTCAAGCCGTAGTGGGGCGACT
Found at i:5925 original size:17 final size:18
Alignment explanation
Indices: 5905--5941 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5895 CTATGTGGTC
5905 TTCATATT-ATTTTCCTT
1 TTCATATTAATTTTCCTT
*
5922 TTCATTTTAATTTTCCTT
1 TTCATATTAATTTTCCTT
5940 TT
1 TT
5942 ATCGAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (18 bp):
TTCATATTAATTTTCCTT
Found at i:6659 original size:13 final size:13
Alignment explanation
Indices: 6641--6667 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6631 TAGTTGATTG
6641 AAATAAAATAAAA
1 AAATAAAATAAAA
6654 AAATAAAATAAAA
1 AAATAAAATAAAA
6667 A
1 A
6668 GTAATTTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAATAAAATAAAA
Found at i:9064 original size:33 final size:34
Alignment explanation
Indices: 9022--9091 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
9012 TTTTGGTGCC
* *
9022 TTGACTTTGTTT-CTTTTTTGGCGTATGAGCATA
1 TTGACTTTGTTTCCCTTTGTGGCGTATGAGCATA
*
9055 TTGACTTTGTTTCCCTTTGTGGCGTATGAGTATA
1 TTGACTTTGTTTCCCTTTGTGGCGTATGAGCATA
9089 TTG
1 TTG
9092 CCAGAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 12 0.36
34 21 0.64
ACGTcount: A:0.14, C:0.13, G:0.23, T:0.50
Consensus pattern (34 bp):
TTGACTTTGTTTCCCTTTGTGGCGTATGAGCATA
Found at i:9703 original size:36 final size:36
Alignment explanation
Indices: 9656--9734 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
9646 GTTTGATGAG
9656 GCTCCTGAGACATCCTCAAGCCGTAGTGGGGCGACT
1 GCTCCTGAGACATCCTCAAGCCGTAGTGGGGCGACT
* *
9692 GCTCCTGAGACATCCTCAAGCCGTGGTGGGGTGACT
1 GCTCCTGAGACATCCTCAAGCCGTAGTGGGGCGACT
9728 GCTCCTG
1 GCTCCTG
9735 GAGCCACACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.16, C:0.30, G:0.32, T:0.22
Consensus pattern (36 bp):
GCTCCTGAGACATCCTCAAGCCGTAGTGGGGCGACT
Found at i:10050 original size:133 final size:133
Alignment explanation
Indices: 9812--10078 Score: 525
Period size: 133 Copynumber: 2.0 Consensus size: 133
9802 AGACCTTCGG
9812 ACCATGCTTTCTATAGGCTTTTGGTTTTACCACCAACTGATCTGAAACTCTTTTTAAGTATATTT
1 ACCATGCTTTCTATAGGCTTTTGGTTTTACCACCAACTGATCTGAAACTCTTTTTAAGTATATTT
9877 AAACTTTAGAGGTAGGGCTATCCCAGACTTGTTCTGATGATGATGTGCTGTTCTCTGAATCATCA
66 AAACTTTAGAGGTAGGGCTATCCCAGACTTGTTCTGATGATGATGTGCTGTTCTCTGAATCATCA
9942 TCC
131 TCC
*
9945 ACCATGTTTTCTATAGGCTTTTGGTTTTACCACCAACTGATCTGAAACTCTTTTTAAGTATATTT
1 ACCATGCTTTCTATAGGCTTTTGGTTTTACCACCAACTGATCTGAAACTCTTTTTAAGTATATTT
10010 AAACTTTAGAGGTAGGGCTATCCCAGACTTGTTCTGATGATGATGTGCTGTTCTCTGAATCATCA
66 AAACTTTAGAGGTAGGGCTATCCCAGACTTGTTCTGATGATGATGTGCTGTTCTCTGAATCATCA
10075 TCC
131 TCC
10078 A
1 A
10079 TTTTGGTTAT
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 133 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (133 bp):
ACCATGCTTTCTATAGGCTTTTGGTTTTACCACCAACTGATCTGAAACTCTTTTTAAGTATATTT
AAACTTTAGAGGTAGGGCTATCCCAGACTTGTTCTGATGATGATGTGCTGTTCTCTGAATCATCA
TCC
Found at i:13990 original size:19 final size:19
Alignment explanation
Indices: 13966--14002 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13956 GTTCACATTG
*
13966 AATATTTTAATTTTTATAA
1 AATATTTTAACTTTTATAA
13985 AATATTTTAACTTTTATA
1 AATATTTTAACTTTTATA
14003 TCTTTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
AATATTTTAACTTTTATAA
Found at i:14289 original size:21 final size:21
Alignment explanation
Indices: 14243--14290 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
14233 TGATGAAGTT
* *
14243 AATTTCTTAATAAATAAATAAC
1 AATTTCTAAATAAAT-AATAAA
14265 AATTTCTAAAATAAAT-ATAAA
1 AATTTCT-AAATAAATAATAAA
14286 AATTT
1 AATTT
14291 ATATCTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 7 0.30
23 7 0.30
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTTCTAAATAAATAATAAA
Found at i:25010 original size:20 final size:22
Alignment explanation
Indices: 24971--25010 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
24961 ATCGGTGTTT
*
24971 TCATTTTTATGTTATTTATTCA
1 TCATTTTAATGTTATTTATTCA
24993 TCATTTTAAT-TT-TTTATT
1 TCATTTTAATGTTATTTATT
25011 TTGTATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.68
Consensus pattern (22 bp):
TCATTTTAATGTTATTTATTCA
Found at i:26881 original size:24 final size:23
Alignment explanation
Indices: 26843--26900 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 23
26833 AAAATTTAAA
*
26843 ATAATAATAATAATTATTATAATT
1 ATAATAA-AAAAATTATTATAATT
26867 ATAATTAAAAAAATTATTATAATT
1 ATAA-TAAAAAAATTATTATAATT
*
26891 TTAATAAAAA
1 ATAATAAAAA
26901 TTTTATGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 6 0.19
24 22 0.71
25 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATAATAAAAAAATTATTATAATT
Found at i:27498 original size:20 final size:20
Alignment explanation
Indices: 27470--27510 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
27460 AAATTAATCG
*
27470 ATAATATAATAGTTAATTAT
1 ATAAAATAATAGTTAATTAT
*
27490 ATAAAATAATATTTAATTAT
1 ATAAAATAATAGTTAATTAT
27510 A
1 A
27511 AATATAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
ATAAAATAATAGTTAATTAT
Found at i:27520 original size:17 final size:18
Alignment explanation
Indices: 27470--27520 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
27460 AAATTAATCG
27470 ATAATATAATAGTTAATTAT
1 ATAATATAAT--TTAATTAT
*
27490 ATAAAATAATATTTAATTAT
1 ATAATAT-A-ATTTAATTAT
27510 A-AATATAATTT
1 ATAATATAATTT
27521 TAAAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 4 0.15
18 1 0.04
19 4 0.15
20 15 0.56
21 1 0.04
22 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
ATAATATAATTTAATTAT
Done.