Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168181.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_419, 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: 27690
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2717 original size:26 final size:26
Alignment explanation
Indices: 2681--2737 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
2671 TCGAATAGAA
2681 CTCATTTTTACAACTGGAGCAAAAAT
1 CTCATTTTTACAACTGGAGCAAAAAT
2707 CTCATTTTTACAACTGGAGCAAAAAT
1 CTCATTTTTACAACTGGAGCAAAAAT
2733 CTCAT
1 CTCAT
2738 CAAAATCGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (26 bp):
CTCATTTTTACAACTGGAGCAAAAAT
Found at i:6763 original size:1 final size:1
Alignment explanation
Indices: 6757--6784 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
6747 ACTTTCTTAG
6757 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
6785 GTCTGAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:9307 original size:14 final size:14
Alignment explanation
Indices: 9285--9319 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
9275 GTTAATTGGT
*
9285 TATGTTTTCTCACA
1 TATGCTTTCTCACA
9299 TATGCTTTCTCACA
1 TATGCTTTCTCACA
9313 TATGCTT
1 TATGCTT
9320 CCTTGGCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.49
Consensus pattern (14 bp):
TATGCTTTCTCACA
Found at i:11115 original size:21 final size:21
Alignment explanation
Indices: 11075--11115 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11065 TTTAGTTAAC
* *
11075 ATATACAAGGAATAGCATAAT
1 ATATACAAGGAACAACATAAT
*
11096 ATATACAAGGAACAATATAA
1 ATATACAAGGAACAACATAA
11116 AAGGTTAGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.22
Consensus pattern (21 bp):
ATATACAAGGAACAACATAAT
Found at i:12446 original size:22 final size:21
Alignment explanation
Indices: 12418--12482 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
12408 TTAATCATAC
12418 AATCACACAAATAAATATATA
1 AATCACACAAATAAATATATA
12439 TAATCACACAAATAACA-ATATA
1 -AATCACACAAATAA-ATATATA
** *
12461 AATCATGCAATTAAATATATA
1 AATCACACAAATAAATATATA
12482 A
1 A
12483 TCATGCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
20 1 0.03
21 17 0.45
22 19 0.50
23 1 0.03
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
AATCACACAAATAAATATATA
Found at i:12496 original size:41 final size:41
Alignment explanation
Indices: 12434--12706 Score: 288
Period size: 41 Copynumber: 6.7 Consensus size: 41
12424 ACAAATAAAT
** * *
12434 ATATATAATCACACAAATAACAATATAAATCATGCAATTAA
1 ATATATAATCATGCAATTAACAATATAAAACATGCAATTAA
*
12475 ATATATAATCATGCAATTAACAACATAAAACATGCAATTAA
1 ATATATAATCATGCAATTAACAATATAAAACATGCAATTAA
* *
12516 ATATATAATCAAGCAATTAACAATATAAAGCATGCAATTAA
1 ATATATAATCATGCAATTAACAATATAAAACATGCAATTAA
* * * * *
12557 ATATATTATCATGCAGTTAACGATATAAAACATACAAATAA
1 ATATATAATCATGCAATTAACAATATAAAACATGCAATTAA
* *
12598 ATATAT--T-ATGCAATTAACGATATAAAACATGCAAATAA
1 ATATATAATCATGCAATTAACAATATAAAACATGCAATTAA
* ** * * *
12636 ATATATTATCATGCAATTAAGTATATAATA-ATACAAAT-A
1 ATATATAATCATGCAATTAACAATATAAAACATGCAATTAA
*
12675 ATAATATAAATCATACAATTAA-ATATATAAAA
1 AT-ATAT-AATCATGCAATTAACA-ATATAAAA
12707 ATAATCAAGC
Statistics
Matches: 201, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
38 35 0.17
39 4 0.02
40 12 0.06
41 150 0.75
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.29
Consensus pattern (41 bp):
ATATATAATCATGCAATTAACAATATAAAACATGCAATTAA
Found at i:12703 original size:120 final size:121
Alignment explanation
Indices: 12424--12706 Score: 297
Period size: 120 Copynumber: 2.3 Consensus size: 121
12414 ATACAATCAC
* * * * *
12424 ACAAATAAATATATATAATCACACAAATAACAATATAAATCATGCAATTAAATATATAATCATGC
1 ACAAATAAA-ATATATAATCATACAATTAA-AATATAAAACATACAAATAAATATAT-ATCATGC
*
12489 AATTAACAACATAAAACATGCAATTAAATATATAATCAAGCAATTAACAATATAAAGCAT
63 AATTAACAACATAAAACATGCAAATAAATATATAATCAAGCAATTAACAATATAAA-CAT
* * * * * *
12549 GC-AATTAAATATATTATCATGCAGTTAACGATATAAAACATACAAATAAATATAT-T-ATGCAA
1 ACAAATAAAATATATAATCATACAATTAA-AATATAAAACATACAAATAAATATATATCATGCAA
* * * * **
12611 TTAACGATATAAAACATGCAAATAAATATATTATCATGCAATTAAGTATATAATA-AT
65 TTAACAACATAAAACATGCAAATAAATATATAATCAAGCAATTAACAATATAA-ACAT
12668 ACAAATAATAATATA-AATCATACAATTAAATATATAAAA
1 ACAAATAA-AATATATAATCATACAATTAAA-ATATAAAA
12707 ATAATCAAGC
Statistics
Matches: 130, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
119 3 0.02
120 75 0.58
121 8 0.06
123 38 0.29
124 5 0.04
125 1 0.01
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (121 bp):
ACAAATAAAATATATAATCATACAATTAAAATATAAAACATACAAATAAATATATATCATGCAAT
TAACAACATAAAACATGCAAATAAATATATAATCAAGCAATTAACAATATAAACAT
Found at i:12754 original size:20 final size:20
Alignment explanation
Indices: 12729--12821 Score: 87
Period size: 20 Copynumber: 4.6 Consensus size: 20
12719 CTATACAAAT
*
12729 AAATAAATTGATAATCATGC
1 AAATAAATTAATAATCATGC
*
12749 AAATAAATTAATAATCATGT
1 AAATAAATTAATAATCATGC
** * *
12769 AAGCATATTAATAGTCATGC
1 AAATAAATTAATAATCATGC
* **
12789 AAATATATTAATAAATCACAC
1 AAATAAATTAAT-AATCATGC
*
12810 AAATATATTAAT
1 AAATAAATTAAT
12822 CATATAAATA
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
20 43 0.72
21 17 0.28
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (20 bp):
AAATAAATTAATAATCATGC
Found at i:12861 original size:16 final size:18
Alignment explanation
Indices: 12842--12882 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
12832 AACTATTAGA
12842 CAAATAA-ATTA-TCATG
1 CAAATAATATTATTCATG
12858 CAAATATAATATTATTCATG
1 C-AA-ATAATATTATTCATG
12878 CAAAT
1 CAAAT
12883 TCATGCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
16 1 0.05
17 2 0.10
18 6 0.29
19 6 0.29
20 6 0.29
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (18 bp):
CAAATAATATTATTCATG
Found at i:12863 original size:32 final size:33
Alignment explanation
Indices: 12808--12871 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 33
12798 AATAAATCAC
* *
12808 ACAAATATATTAATCATATAAATA-AACTATTAG
1 ACAAATAAATTAATCATACAAATATAA-TATTAG
*
12841 ACAAATAAATT-ATCATGCAAATATAATATTA
1 ACAAATAAATTAATCATACAAATATAATATTA
12872 TTCATGCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 15 0.56
33 12 0.44
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (33 bp):
ACAAATAAATTAATCATACAAATATAATATTAG
Found at i:12878 original size:20 final size:18
Alignment explanation
Indices: 12845--12882 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
12835 TATTAGACAA
12845 ATAAATTATCATGCAAAT
1 ATAAATTATCATGCAAAT
12863 ATAATATTATTCATGCAAAT
1 ATAA-ATTA-TCATGCAAAT
12883 TCATGCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (18 bp):
ATAAATTATCATGCAAAT
Found at i:17915 original size:12 final size:11
Alignment explanation
Indices: 17895--17959 Score: 64
Period size: 11 Copynumber: 6.2 Consensus size: 11
17885 CCAAACTGCA
*
17895 TTTAAAATTTT
1 TTTAAAAATTT
17906 TTTAAAAATTT
1 TTTAAAAATTT
* *
17917 TTTAGAAATCT
1 TTTAAAAATTT
*
17928 TTTAGAAA-TT
1 TTTAAAAATTT
17938 TTT-AAAATTT
1 TTTAAAAATTT
*
17948 TTT-GAAATTT
1 TTTAAAAATTT
17958 TT
1 TT
17960 ACAATTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
9 3 0.06
10 17 0.36
11 27 0.57
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (11 bp):
TTTAAAAATTT
Found at i:17949 original size:10 final size:10
Alignment explanation
Indices: 17895--18036 Score: 89
Period size: 10 Copynumber: 14.2 Consensus size: 10
17885 CCAAACTGCA
17895 TTTAAAATTTT
1 TTTAAAA-TTT
17906 TTTAAAAATTT
1 TTT-AAAATTT
*
17917 TTTAGAAATCT
1 TTTA-AAATTT
17928 TTTAGAAA-TT
1 TTTA-AAATTT
17938 TTTAAAATTT
1 TTTAAAATTT
*
17948 TTTGAAA-TT
1 TTTAAAATTT
*
17957 TTTACAATTT
1 TTTAAAATTT
*
17967 TTTGAAA-TT
1 TTTAAAATTT
*
17976 TTTACAATTTTT
1 TTTA-AA-ATTT
*
17988 TTTGAAA-TT
1 TTTAAAATTT
* *
17997 TTAAAAATTA
1 TTTAAAATTT
*
18007 TTT--AATTA
1 TTTAAAATTT
*
18015 TTTATAATTT
1 TTTAAAATTT
*
18025 TTAAAAATTT
1 TTTAAAATTT
18035 TT
1 TT
18037 AGAAAATTTC
Statistics
Matches: 103, Mismatches: 18, Indels: 21
0.73 0.13 0.15
Matches are distributed among these distances:
8 8 0.08
9 22 0.21
10 40 0.39
11 24 0.23
12 9 0.09
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (10 bp):
TTTAAAATTT
Found at i:17954 original size:19 final size:19
Alignment explanation
Indices: 17895--18037 Score: 119
Period size: 19 Copynumber: 7.2 Consensus size: 19
17885 CCAAACTGCA
*
17895 TTTAAAATTTTTTTAAAAATTT
1 TTTAAAA-TTTTTT-GAAA-TT
*
17917 TTTAGAAATCTTTTAGAAATT
1 TTTA-AAAT-TTTTTGAAATT
17938 TTTAAAATTTTTTGAAATT
1 TTTAAAATTTTTTGAAATT
*
17957 TTTACAATTTTTTGAAATT
1 TTTAAAATTTTTTGAAATT
*
17976 TTTACAATTTTTTTTGAAATT
1 TTTA-AA-ATTTTTTGAAATT
* *
17997 TTAAAAATTATTT--AATT
1 TTTAAAATTTTTTGAAATT
* **
18014 ATTTATAATTTTTAAAAATT
1 -TTTAAAATTTTTTGAAATT
18034 TTTA
1 TTTA
18038 GAAAATTTCA
Statistics
Matches: 101, Mismatches: 13, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
17 4 0.04
18 9 0.09
19 41 0.41
20 11 0.11
21 21 0.21
22 8 0.08
23 7 0.07
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTAAAATTTTTTGAAATT
Found at i:18042 original size:11 final size:10
Alignment explanation
Indices: 17904--18060 Score: 78
Period size: 10 Copynumber: 15.9 Consensus size: 10
17894 ATTTAAAATT
17904 TTTTTAAAAA
1 TTTTTAAAAA
*
17914 TTTTTTAGAAA
1 -TTTTTAAAAA
*
17925 TCTTTTAGAAA
1 T-TTTTAAAAA
17936 TTTTT-AAAA
1 TTTTTAAAAA
**
17945 TTTTTTGAAA
1 TTTTTAAAAA
*
17955 TTTTT-ACAA
1 TTTTTAAAAA
**
17964 TTTTTTGAAA
1 TTTTTAAAAA
**
17974 TTTTTACAATT
1 TTTTTA-AAAA
**
17985 TTTTTTGAAA
1 TTTTTAAAAA
17995 -TTTTAAAAA
1 TTTTTAAAAA
18004 TTATTT---AA
1 TT-TTTAAAAA
*
18012 TTATTT-ATAA
1 TT-TTTAAAAA
18022 TTTTTAAAAA
1 TTTTTAAAAA
18032 TTTTTAGAAAA
1 TTTTTA-AAAA
*
18043 -TTTCAAAAA
1 TTTTTAAAAA
*
18052 ATTTTAAAA
1 TTTTTAAAA
18061 TCTTTTAGAA
Statistics
Matches: 115, Mismatches: 20, Indels: 23
0.73 0.13 0.15
Matches are distributed among these distances:
8 8 0.07
9 29 0.25
10 46 0.40
11 32 0.28
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.53
Consensus pattern (10 bp):
TTTTTAAAAA
Found at i:20151 original size:12 final size:12
Alignment explanation
Indices: 20132--20162 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20122 TAAAAAATTT
20132 AATTTAATAAAA
1 AATTTAATAAAA
*
20144 ATTTTAATAAAA
1 AATTTAATAAAA
20156 AATTTAA
1 AATTTAA
20163 ATTGATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATTTAATAAAA
Found at i:20185 original size:29 final size:29
Alignment explanation
Indices: 20122--20179 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
20112 GAGATTTTTT
*
20122 TAAAAAATTTAATTTAATAAAAATTTTAA
1 TAAAAAATTTAAATTAATAAAAATTTTAA
*
20151 TAAAAAATTTAAATTGAT-AAAA-TTTAA
1 TAAAAAATTTAAATTAATAAAAATTTTAA
20178 TA
1 TA
20180 TGAAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 7 0.26
28 4 0.15
29 16 0.59
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
TAAAAAATTTAAATTAATAAAAATTTTAA
Found at i:20279 original size:13 final size:13
Alignment explanation
Indices: 20242--20302 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 13
20232 TTTTCAATGA
20242 TAAAAAT-TTTAT
1 TAAAAATATTTAT
* *
20254 TAATAGT-TTTAT
1 TAAAAATATTTAT
20266 TAAAAATATTTATT
1 TAAAAATATTTA-T
*
20280 TAAAAA-ATATAT
1 TAAAAATATTTAT
20292 TAAAATATATT
1 TAAAA-ATATT
20303 AAAATTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 21 0.54
13 9 0.23
14 9 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
TAAAAATATTTAT
Found at i:20298 original size:10 final size:10
Alignment explanation
Indices: 20283--20307 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20273 ATTTATTTAA
20283 AAAATATATT
1 AAAATATATT
20293 AAAATATATT
1 AAAATATATT
20303 AAAAT
1 AAAAT
20308 TTTTTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATATATT
Found at i:20367 original size:21 final size:20
Alignment explanation
Indices: 20343--20382 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
20333 TATGTGATGA
20343 GATTTTTAATTAATTAATTTT
1 GATTTTTAATT-ATTAATTTT
*
20364 GATTTTTAATTTTTAATTT
1 GATTTTTAATTATTAATTT
20383 AATTTAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (20 bp):
GATTTTTAATTATTAATTTT
Done.