Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168162.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_401, 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: 28672
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:4235 original size:248 final size:248
Alignment explanation
Indices: 3797--4293 Score: 976
Period size: 248 Copynumber: 2.0 Consensus size: 248
3787 TAAAAATTTC
3797 ATGCACATGCCTGCTTCAGGTGTATATAATAAACCTCTCTATGCATGAAATCAGTACCATCTCAC
1 ATGCACATGCCTGCTTCAGGTGTATATAATAAACCTCTCTATGCATGAAATCAGTACCATCTCAC
3862 AAAGAGAGATGCATAAAAAGATGCAGAAATAAGCATAAATAAACTCAGTAAACACACACTTACAA
66 AAAGAGAGATGCATAAAAAGATGCAGAAATAAGCATAAATAAACTCAGTAAACACACACTTACAA
3927 GACAAAAGAATGTCTTTTAAGGCTCATAGTTATCGAGTATTATGTAATTTTCCATGCATAATGAG
131 GACAAAAGAATGTCTTTTAAGGCTCATAGTTATCGAGTATTATGTAATTTTCCATGCATAATGAG
*
3992 ACTGATAACACATGCAGATTAGTTTGAGACAAGAAAAGAGTGGCACTCTTTAG
196 ACTGATAACACATGCAGATTAGTTTGAGACAAAAAAAGAGTGGCACTCTTTAG
4045 ATGCACATGCCTGCTTCAGGTGTATATAATAAACCTCTCTATGCATGAAATCAGTACCATCTCAC
1 ATGCACATGCCTGCTTCAGGTGTATATAATAAACCTCTCTATGCATGAAATCAGTACCATCTCAC
4110 AAAGAGAGATGCATAAAAAGATGCAGAAATAAGCATAAATAAACTCAGTAAACACACACTTACAA
66 AAAGAGAGATGCATAAAAAGATGCAGAAATAAGCATAAATAAACTCAGTAAACACACACTTACAA
4175 GACAAAAGAATGTCTTTTAAGGCTCATAGTTATCGAGTATTATGTAATTTTCCATGCATAATGAG
131 GACAAAAGAATGTCTTTTAAGGCTCATAGTTATCGAGTATTATGTAATTTTCCATGCATAATGAG
*
4240 ACTGATAACGCATGCAGATTAGTTTGAGACAAAAAAAGAGTGGCACTCTTTAG
196 ACTGATAACACATGCAGATTAGTTTGAGACAAAAAAAGAGTGGCACTCTTTAG
4293 A
1 A
4294 AGTATAAACC
Statistics
Matches: 247, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
248 247 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (248 bp):
ATGCACATGCCTGCTTCAGGTGTATATAATAAACCTCTCTATGCATGAAATCAGTACCATCTCAC
AAAGAGAGATGCATAAAAAGATGCAGAAATAAGCATAAATAAACTCAGTAAACACACACTTACAA
GACAAAAGAATGTCTTTTAAGGCTCATAGTTATCGAGTATTATGTAATTTTCCATGCATAATGAG
ACTGATAACACATGCAGATTAGTTTGAGACAAAAAAAGAGTGGCACTCTTTAG
Found at i:6456 original size:18 final size:20
Alignment explanation
Indices: 6430--6471 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
6420 TTTAATTATC
6430 ATATAAATAATTT-TT-TAA
1 ATATAAATAATTTATTATAA
* *
6448 ATATGAATATTTTATTATAA
1 ATATAAATAATTTATTATAA
6468 ATAT
1 ATAT
6472 TTTTTCTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 11 0.55
19 2 0.10
20 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATATAAATAATTTATTATAA
Found at i:16916 original size:4 final size:4
Alignment explanation
Indices: 16907--16940 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
16897 AGTTTACAAA
* *
16907 ATGT ATGT ATGT ATAT ATGT ATGT ATAT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
16941 TTGGTACATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:16927 original size:12 final size:12
Alignment explanation
Indices: 16910--16940 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
16900 TTACAAAATG
16910 TATGTATGTATA
1 TATGTATGTATA
16922 TATGTATGTATA
1 TATGTATGTATA
16934 TATGTAT
1 TATGTAT
16941 TTGGTACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TATGTATGTATA
Found at i:16997 original size:25 final size:25
Alignment explanation
Indices: 16962--17011 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
16952 GAGCAGACTA
16962 AGTCGGAAAAATTACACAAGATGTT
1 AGTCGGAAAAATTACACAAGATGTT
*
16987 AGTCGGCAAAATTACACAAGATGTT
1 AGTCGGAAAAATTACACAAGATGTT
17012 TCGTTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (25 bp):
AGTCGGAAAAATTACACAAGATGTT
Found at i:23477 original size:16 final size:16
Alignment explanation
Indices: 23456--23487 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
23446 AATCAAAGTG
*
23456 AATTTTTATTTAATTT
1 AATTTTAATTTAATTT
23472 AATTTTAATTTAATTT
1 AATTTTAATTTAATTT
23488 TTTAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
AATTTTAATTTAATTT
Found at i:23478 original size:11 final size:11
Alignment explanation
Indices: 23464--23488 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
23454 TGAATTTTTA
23464 TTTAATTTAAT
1 TTTAATTTAAT
23475 TTTAATTTAAT
1 TTTAATTTAAT
23486 TTT
1 TTT
23489 TTAATTTTTA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTAATTTAAT
Found at i:24445 original size:18 final size:18
Alignment explanation
Indices: 24397--24448 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
24387 ATACTATTTG
24397 ATAAATTATTATTTTTATTA
1 ATAAATTATTA--TTTATTA
* *
24417 AT-TATCAATTATTTATTA
1 ATAAAT-TATTATTTATTA
24435 ATAAATTATTATTT
1 ATAAATTATTATTT
24449 GACATAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
18 16 0.62
19 4 0.15
20 6 0.23
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
ATAAATTATTATTTATTA
Found at i:24474 original size:14 final size:14
Alignment explanation
Indices: 24442--24471 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
24432 TTAATAAATT
24442 ATTATTTGACATAA
1 ATTATTTGACATAA
24456 ATTATTTGA-ATAA
1 ATTATTTGACATAA
24469 ATT
1 ATT
24472 TATAATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (14 bp):
ATTATTTGACATAA
Found at i:24494 original size:19 final size:20
Alignment explanation
Indices: 24455--24495 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
24445 ATTTGACATA
24455 AATTATTTGAATAAATTTAT
1 AATTATTTGAATAAATTTAT
* *
24475 AATTATTT-ATTAATTTTAT
1 AATTATTTGAATAAATTTAT
24494 AA
1 AA
24496 ATTTTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
AATTATTTGAATAAATTTAT
Found at i:24498 original size:20 final size:21
Alignment explanation
Indices: 24452--24498 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
24442 ATTATTTGAC
24452 ATAAATTATTTGAATAAATTT
1 ATAAATTATTTGAATAAATTT
* *
24473 AT-AATTATTT-ATTAATTTT
1 ATAAATTATTTGAATAAATTT
24492 ATAAATT
1 ATAAATT
24499 TTAAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 9 0.39
20 12 0.52
21 2 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATAAATTATTTGAATAAATTT
Found at i:24504 original size:34 final size:33
Alignment explanation
Indices: 24466--24540 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 33
24456 ATTATTTGAA
* *
24466 TAAATTTATAATTATTTATTAATTTTATA-AATTT
1 TAAATTTATAA-AATTT-TTAATTATATATAATTT
* *
24500 TAAATTTTTAAAATTTTTTATTATATATAATTT
1 TAAATTTATAAAATTTTTAATTATATATAATTT
*
24533 TTAATTTA
1 TAAATTTA
24541 ATATCTTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
32 9 0.26
33 15 0.44
34 10 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (33 bp):
TAAATTTATAAAATTTTTAATTATATATAATTT
Found at i:24507 original size:16 final size:16
Alignment explanation
Indices: 24479--24539 Score: 61
Period size: 16 Copynumber: 3.7 Consensus size: 16
24469 ATTTATAATT
24479 ATTTATTAATTTTATAA
1 ATTT-TTAATTTTATAA
*
24496 ATTTTAAATTTT-TAAA
1 ATTTTTAATTTTAT-AA
* *
24512 ATTTTTTATTATATATA
1 ATTTTTAATTTTATA-A
24529 ATTTTTAATTT
1 ATTTTTAATTT
24540 AATATCTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 1 0.03
16 19 0.54
17 15 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTTAATTTTATAA
Found at i:27155 original size:24 final size:23
Alignment explanation
Indices: 27107--27157 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
27097 AACCACAAGT
27107 ATAAAAGTAGTCTGGCTGTTAAA
1 ATAAAAGTAGTCTGGCTGTTAAA
*
27130 ATAAAAGTACCGTC-GGTTGTTAAA
1 ATAAAAGTA--GTCTGGCTGTTAAA
27154 ATAA
1 ATAA
27158 TTTAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 9 0.36
24 13 0.52
25 3 0.12
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (23 bp):
ATAAAAGTAGTCTGGCTGTTAAA
Found at i:27190 original size:34 final size:34
Alignment explanation
Indices: 27125--27191 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
27115 AGTCTGGCTG
* *
27125 TTAAAATAAAAGTACCGTCGGTTGTTAAAATAAT
1 TTAAAATAAAAGTACCGTCAGCTGTTAAAATAAT
* * *
27159 TTAAAATAAAAGTACTGTTAGCTGTTGAAATAA
1 TTAAAATAAAAGTACCGTCAGCTGTTAAAATAA
27192 AATTTTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (34 bp):
TTAAAATAAAAGTACCGTCAGCTGTTAAAATAAT
Done.