Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168000.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_256, 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: 41964
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:9501 original size:2 final size:2
Alignment explanation
Indices: 9494--9545 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
9484 CCATAAATTC
9494 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
9536 AG AG AG AG AG
1 AG AG AG AG AG
9546 CATGCCACAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10637 original size:18 final size:19
Alignment explanation
Indices: 10591--10639 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
10581 TTTTAGTGAG
10591 AAAAATTAAAG-TGTCACT
1 AAAAATTAAAGTTGTCACT
* *
10609 AAAAGATTAAAGTTTTTAC-
1 AAAA-ATTAAAGTTGTCACT
10628 AAAAATTAAAGT
1 AAAAATTAAAGT
10640 AGCCCAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 12 0.44
19 11 0.41
20 4 0.15
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.31
Consensus pattern (19 bp):
AAAAATTAAAGTTGTCACT
Found at i:11788 original size:246 final size:244
Alignment explanation
Indices: 11357--11852 Score: 774
Period size: 246 Copynumber: 2.0 Consensus size: 244
11347 GATGTAGATT
* *
11357 ATTTTTGTTTGCTTCCCATCCAGCCCATGTTATTTAACGAGTGGACCACTTGTTCATTCTTTTTT
1 ATTTTTGTTTGCTTCCAATCCAACCCATGTTATTTAACGAGTGGACCACTTGTTCATTCTTTTTT
11422 TTTCAAATCATTTAGTCTATTTGAAAAGTAGATTTTATAATTTAAAAATGAATGATATTATATAA
66 TTTCAAATCATTTAGTCTATTTGAAAAGTAGATTTTATAATTTAAAAATGAATGATATTATATAA
11487 AAATAAAACATAAAAATAATAAGATTTAAAATTTTAATAATAATTATATATAAATTTAATAAAAT
131 AAATAAAACATAAAAATAATAAGATTTAAAATTTTAATAATAATTATATATAAATTTAATAAAAT
* * * **
11552 TAAAAATATATATTTTATA-TTTTGTATCGACATAAATTGTGATATATA
196 TAAAAATATATATTATATATTTTTATATCGACACAAATCATGATATATA
11600 ATTTTTGTTTGC-TCCAATCCAACCCATGTTA-TTAACGAGTGGGACTCACTTGTTCATTCATTT
1 ATTTTTGTTTGCTTCCAATCCAACCCATGTTATTTAACGAGT-GGAC-CACTTGTTCATTC-TTT
11663 TCTTTTTC-AATCAATTTAGTC-A-TTG-AAAGTAGATTTTATAATTTAAAAAATGACATGAATA
63 T-TTTTTCAAATC-ATTTAGTCTATTTGAAAAGTAGATTTTATAATTT-AAAAATGA-ATG-ATA
*
11724 TTATATAAAAATAAAAACATAAAAGTAATATAG-TTTAAAATTTTAATAATAATTATATATAAAT
123 TTATATAAAAAT-AAAACATAAAAATAATA-AGATTTAAAATTTTAATAATAATTATATATAAAT
11788 TTAATAAAATTAAAAATATATATTATATATTTTTATATCGACACAAATCATGATATATA
186 TTAATAAAATTAAAAATATATATTATATATTTTTATATCGACACAAATCATGATATATA
11847 ATTTTT
1 ATTTTT
11853 ATATAAAATA
Statistics
Matches: 234, Mismatches: 8, Indels: 18
0.90 0.03 0.07
Matches are distributed among these distances:
241 9 0.04
242 40 0.17
243 36 0.15
244 12 0.05
245 29 0.12
246 75 0.32
247 33 0.14
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (244 bp):
ATTTTTGTTTGCTTCCAATCCAACCCATGTTATTTAACGAGTGGACCACTTGTTCATTCTTTTTT
TTTCAAATCATTTAGTCTATTTGAAAAGTAGATTTTATAATTTAAAAATGAATGATATTATATAA
AAATAAAACATAAAAATAATAAGATTTAAAATTTTAATAATAATTATATATAAATTTAATAAAAT
TAAAAATATATATTATATATTTTTATATCGACACAAATCATGATATATA
Found at i:13321 original size:20 final size:21
Alignment explanation
Indices: 13283--13323 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
13273 TATATGTTAT
* *
13283 TTTAATATAATTTTTAATATA
1 TTTAATATAAATTTAAATATA
13304 TTTAA-ATAAATTTAAATATA
1 TTTAATATAAATTTAAATATA
13324 AAATTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATATAAATTTAAATATA
Found at i:13930 original size:13 final size:13
Alignment explanation
Indices: 13909--13984 Score: 57
Period size: 13 Copynumber: 5.8 Consensus size: 13
13899 ATATGATATA
13909 AAAATAATATAAAT
1 AAAA-AATATAAAT
13923 AAAAAATAT-AAT
1 AAAAAATATAAAT
** * *
13935 TTAAAATTTTAAT
1 AAAAAATATAAAT
*
13948 AAAAATTATAAAT
1 AAAAAATATAAAT
*
13961 AAACTTAATA-AAAT
1 AAA--AAATATAAAT
13975 AAAAAATATA
1 AAAAAATATA
13985 TATTTTATAT
Statistics
Matches: 47, Mismatches: 11, Indels: 9
0.70 0.16 0.13
Matches are distributed among these distances:
12 13 0.28
13 20 0.43
14 11 0.23
15 3 0.06
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAAATATAAAT
Found at i:13930 original size:29 final size:28
Alignment explanation
Indices: 13898--13987 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 28
13888 ATAAAATGAT
13898 AATATGATATAAAAATAATATAAATAAAA
1 AATAT-ATATAAAAATAATATAAATAAAA
* *
13927 AATATA-ATTTAAAAT--T-TTAATAAAA
1 AATATATA-TAAAAATAATATAAATAAAA
* * **
13952 ATTATAAATAAACTTAATA-AAATAAAA
1 AATATATATAAAAATAATATAAATAAAA
13979 AATATATAT
1 AATATATAT
13988 TTTATATTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
25 17 0.36
26 2 0.04
27 16 0.34
28 7 0.15
29 5 0.11
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (28 bp):
AATATATATAAAAATAATATAAATAAAA
Found at i:15772 original size:21 final size:19
Alignment explanation
Indices: 15744--15790 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 19
15734 AAATTTCTTG
15744 ATTTTTTTTATTTATTAGAA
1 ATTTTTTTTATTTATTA-AA
*
15764 ATTATTTTTTATTTTTTAAA
1 ATT-TTTTTTATTTATTAAA
15784 ATTTTTT
1 ATTTTTT
15791 CGAGAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 4 0.16
20 8 0.32
21 13 0.52
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
ATTTTTTTTATTTATTAAA
Found at i:17442 original size:20 final size:21
Alignment explanation
Indices: 17405--17457 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
17395 CACTAGCTTT
*
17405 TTTTTGTTTTTATATTTTGTA
1 TTTTTGTATTTATATTTTGTA
*
17426 TTTTTGTATTTAT-TTTTTTA
1 TTTTTGTATTTATATTTTGTA
*
17446 TTATTGTATTTA
1 TTTTTGTATTTA
17458 ATAATATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (21 bp):
TTTTTGTATTTATATTTTGTA
Found at i:23653 original size:26 final size:25
Alignment explanation
Indices: 23607--23658 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
23597 CATTAAATTA
* *
23607 TTTTTATTTTTAAGTTTATATTTAAT
1 TTTTTATTTTAAAGTTAATA-TTAAT
23633 TTTTTA-TTTAAACGTTAATATTAAT
1 TTTTTATTTTAAA-GTTAATATTAAT
23658 T
1 T
23659 ATTAACAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTATTTTAAAGTTAATATTAAT
Found at i:30395 original size:17 final size:17
Alignment explanation
Indices: 30361--30392 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
30351 GAAATAAAAT
30361 AATTTATTTTATATTTG
1 AATTTATTTTATATTTG
30378 AATTT-TTTTATATTT
1 AATTTATTTTATATTT
30393 TGATTAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
AATTTATTTTATATTTG
Found at i:36194 original size:40 final size:40
Alignment explanation
Indices: 36150--36232 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
36140 CACACCATAC
* *
36150 AAAATGAAATTTCAATTTTGTTTAACTCATGAACCACTAA
1 AAAATGAAAATTCAAATTTGTTTAACTCATGAACCACTAA
36190 AAAATGAAAATTCAAATTTGTTTAACTCATGAACCACTAA
1 AAAATGAAAATTCAAATTTGTTTAACTCATGAACCACTAA
36230 AAA
1 AAA
36233 TTCTAGAGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.31
Consensus pattern (40 bp):
AAAATGAAAATTCAAATTTGTTTAACTCATGAACCACTAA
Found at i:37261 original size:13 final size:14
Alignment explanation
Indices: 37243--37274 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
37233 TAGTTTATTA
37243 ATTTTTTAAAT-TT
1 ATTTTTTAAATGTT
37256 ATTTTTTAAATGTT
1 ATTTTTTAAATGTT
37270 ATTTT
1 ATTTT
37275 AATATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (14 bp):
ATTTTTTAAATGTT
Found at i:37310 original size:20 final size:21
Alignment explanation
Indices: 37272--37312 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
37262 TAAATGTTAT
* *
37272 TTTAATATAATTTTTAATATA
1 TTTAATATAAATTTAAATATA
37293 TTTAA-ATAAATTTAAATATA
1 TTTAATATAAATTTAAATATA
37313 AAATTATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATATAAATTTAAATATA
Found at i:37919 original size:13 final size:13
Alignment explanation
Indices: 37898--37973 Score: 57
Period size: 13 Copynumber: 5.8 Consensus size: 13
37888 ATACGATGTA
37898 AAAATAATATAAAT
1 AAAA-AATATAAAT
37912 AAAAAATAT-AAT
1 AAAAAATATAAAT
** * *
37924 TTAAAATTTTAAT
1 AAAAAATATAAAT
*
37937 AAAAATTATAAAT
1 AAAAAATATAAAT
*
37950 AAACTTAATA-AAAT
1 AAA--AAATATAAAT
37964 AAAAAATATA
1 AAAAAATATA
37974 TATTTTATAT
Statistics
Matches: 47, Mismatches: 11, Indels: 9
0.70 0.16 0.13
Matches are distributed among these distances:
12 13 0.28
13 20 0.43
14 11 0.23
15 3 0.06
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAAATATAAAT
Found at i:41395 original size:20 final size:19
Alignment explanation
Indices: 41361--41410 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
41351 TGGCTTTTTT
*
41361 TTTTGTTTTTATTTTTGTA
1 TTTTGTATTTATTTTTGTA
41380 TTTTGTATTTATTTTTGTA
1 TTTTGTATTTATTTTTGTA
41399 TTATTGTATTTA
1 TT-TTGTATTTA
41411 ATAATATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 20 0.69
20 9 0.31
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.74
Consensus pattern (19 bp):
TTTTGTATTTATTTTTGTA
Done.