Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168358.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_579, 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: 22515
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:3121 original size:22 final size:21
Alignment explanation
Indices: 3095--3146 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3085 AAGGATTAAA
*
3095 ATTATATTGTTATTCT-ATATTT
1 ATTATATT-TAATTCTAATA-TT
3117 ATTATATTTAATTCTAATATT
1 ATTATATTTAATTCTAATATT
3138 ATT-TATTTA
1 ATTATATTTA
3147 TTTTTTAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 6 0.21
21 11 0.39
22 11 0.39
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTATATTTAATTCTAATATT
Found at i:3641 original size:2 final size:2
Alignment explanation
Indices: 3634--3663 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3624 AAATATTGTT
3634 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3664 CACACACCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4560 original size:58 final size:58
Alignment explanation
Indices: 4436--4560 Score: 137
Period size: 58 Copynumber: 2.2 Consensus size: 58
4426 TTAATTTTTT
* * ** * *
4436 GTTATAAATTTGTTGAAATTTGTTTGGTTTTAGTTACCAATTTGTTGAGTTTTTGTTG
1 GTTATATATATGTTGAAATTTGTTTGGTTTTAGTTACCAATTTGTTGAGAATTTGCTA
* * *
4494 GTTCTATATATGTTGAAATTTGTTTAGGTTTTGGTTA-TATATTTGTTGA-AATTTGCTA
1 GTTATATATATGTTGAAATTTGTTT-GGTTTTAGTTACCA-ATTTGTTGAGAATTTGCTA
4552 GTTATATAT
1 GTTATATAT
4561 TTTGTTGGAT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
58 36 0.65
59 19 0.35
ACGTcount: A:0.23, C:0.03, G:0.19, T:0.54
Consensus pattern (58 bp):
GTTATATATATGTTGAAATTTGTTTGGTTTTAGTTACCAATTTGTTGAGAATTTGCTA
Found at i:4914 original size:20 final size:20
Alignment explanation
Indices: 4891--4937 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
4881 ATTATATATA
4891 TATATATATTTGAAGTAATT
1 TATATATATTTGAAGTAATT
* * *
4911 TATATTTGTTTGAATTAATT
1 TATATATATTTGAAGTAATT
4931 TATATAT
1 TATATAT
4938 TTGATAGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (20 bp):
TATATATATTTGAAGTAATT
Found at i:11875 original size:19 final size:19
Alignment explanation
Indices: 11839--11875 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11829 AAGGTTTGAA
* *
11839 AATAATTACAATTGTTTTG
1 AATAATTACAAATATTTTG
11858 AATAATTACAAATATTTT
1 AATAATTACAAATATTTT
11876 TATTCAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (19 bp):
AATAATTACAAATATTTTG
Found at i:12044 original size:26 final size:26
Alignment explanation
Indices: 12015--12066 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
12005 TATCGATGGT
12015 TTATCAAAGAAAAATTTCGTAAGTAA
1 TTATCAAAGAAAAATTTCGTAAGTAA
* *
12041 TTATCAATGAAAAATTTCGTAGGTAA
1 TTATCAAAGAAAAATTTCGTAAGTAA
12067 AACTATTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (26 bp):
TTATCAAAGAAAAATTTCGTAAGTAA
Found at i:14032 original size:20 final size:19
Alignment explanation
Indices: 13996--14043 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
13986 TTAATTACAT
*
13996 TTTATTTATAATTTTTTCAA
1 TTTATTT-TAATTTTTTAAA
*
14016 TTTATTTTATTTATTTTAAA
1 TTTATTTTAATT-TTTTAAA
*
14036 TTTGTTTT
1 TTTATTTT
14044 TAAAATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTATTTTAATTTTTTAAA
Found at i:17097 original size:12 final size:12
Alignment explanation
Indices: 17082--17119 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
17072 TAATTATTAA
17082 TATTATTAATAT
1 TATTATTAATAT
*
17094 TATTATTAAAAT
1 TATTATTAATAT
17106 TATTATTAATAT
1 TATTATTAATAT
17118 TA
1 TA
17120 AACTAGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTATTAATAT
Found at i:17107 original size:18 final size:18
Alignment explanation
Indices: 17086--17121 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17076 TATTAATATT
*
17086 ATTAATATTATTATTAAA
1 ATTAATATTAATATTAAA
*
17104 ATTATTATTAATATTAAA
1 ATTAATATTAATATTAAA
17122 CTAGAAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTAATATTAATATTAAA
Found at i:17119 original size:9 final size:9
Alignment explanation
Indices: 17074--17098 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
17064 TTTTTTTTTA
17074 ATTATTAAT
1 ATTATTAAT
17083 ATTATTAAT
1 ATTATTAAT
17092 ATTATTA
1 ATTATTA
17099 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTATTAAT
Found at i:17129 original size:24 final size:24
Alignment explanation
Indices: 17082--17129 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
17072 TAATTATTAA
* *
17082 TATTATTAATATTATTATTAAAAT
1 TATTATTAATATTATAACTAAAAT
17106 TATTATTAATATTA-AACTAGAAAT
1 TATTATTAATATTATAACTA-AAAT
17130 GAAGACAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
TATTATTAATATTATAACTAAAAT
Found at i:17364 original size:46 final size:46
Alignment explanation
Indices: 17296--17383 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
17286 TTTATTATTG
* *
17296 AAAAGCTCCTCTCAATAGAGGCTCAACAACTTTAAAATTCTCTTGA
1 AAAAGCTCATCTCAATAAAGGCTCAACAACTTTAAAATTCTCTTGA
*
17342 AAAAGCTCATCTCAGTAAAGGCTCAACAACTTTAAAATTCTC
1 AAAAGCTCATCTCAATAAAGGCTCAACAACTTTAAAATTCTC
17384 ATCTTGGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (46 bp):
AAAAGCTCATCTCAATAAAGGCTCAACAACTTTAAAATTCTCTTGA
Found at i:17400 original size:25 final size:25
Alignment explanation
Indices: 17366--17414 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
17356 GTAAAGGCTC
17366 AACAACTTTAAAATTCTCATCTTGG
1 AACAACTTTAAAATTCTCATCTTGG
17391 AACAACTTTAAAATTCTCATCTTG
1 AACAACTTTAAAATTCTCATCTTG
17415 AAAAAGCTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (25 bp):
AACAACTTTAAAATTCTCATCTTGG
Found at i:17438 original size:74 final size:70
Alignment explanation
Indices: 17320--17460 Score: 219
Period size: 74 Copynumber: 2.0 Consensus size: 70
17310 ATAGAGGCTC
*
17320 AACAACTTTAAAATTCTCTTGAAAAAGCTCATCTCAGTAAAGGCTCAACAACTTTAAAATTCTCA
1 AACAACTTTAAAATTCTCTTGAAAAAGCTCATCTCAGCAAAGGCTCAACAACTTTAAAATT-TCA
17385 TCTTGG
65 TCTTGG
* *
17391 AACAACTTTAAAATTCTCATCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTT
1 AACAACTTTAAAA-T-TC-TCTTGAAAAAGCTCATCTCAGCAAAGGCTCAACAACTTTAAAATTT
17456 CATCT
63 CATCT
17461 AAAAAAGCTC
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
71 13 0.20
72 1 0.02
73 8 0.12
74 42 0.66
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.30
Consensus pattern (70 bp):
AACAACTTTAAAATTCTCTTGAAAAAGCTCATCTCAGCAAAGGCTCAACAACTTTAAAATTTCAT
CTTGG
Found at i:17478 original size:47 final size:49
Alignment explanation
Indices: 17391--17506 Score: 191
Period size: 47 Copynumber: 2.4 Consensus size: 49
17381 CTCATCTTGG
* *
17391 AACAACTTTAAAATTCTCATCTTGAAAAAGCTCCTCTCAGCAGAGGCTC
1 AACAACTTTAAAATTCTCATCTTAAAAAAGCTCCTCTCAGCAAAGGCTC
*
17440 AACAACTTTAAAATT-TCATC-TAAAAAAGCTCCTTTCAGCAAAGGCTC
1 AACAACTTTAAAATTCTCATCTTAAAAAAGCTCCTCTCAGCAAAGGCTC
17487 AACAACTTTAAAATTCTCAT
1 AACAACTTTAAAATTCTCAT
17507 TTTTTTCAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
47 39 0.62
48 9 0.14
49 15 0.24
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (49 bp):
AACAACTTTAAAATTCTCATCTTAAAAAAGCTCCTCTCAGCAAAGGCTC
Found at i:17521 original size:120 final size:119
Alignment explanation
Indices: 17296--17532 Score: 325
Period size: 120 Copynumber: 2.0 Consensus size: 119
17286 TTTATTATTG
* * *
17296 AAAAGCTCCTCTCAATAGAGGCTCAACAACTTTAAAATTCTCTTGAAAAAGCTCATCTCAGTAAA
1 AAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATTCTCTTAAAAAAGCTCATCTCAGCAAA
*
17361 GGCTCAACAACTTTAAAATTCTCATCTTGGAACAACTTTAAAATTCTCATCTTGA
66 GGCTCAACAACTTTAAAATTCTCATCTTGGAACAAATTT-AAATTCTCATCTTGA
* * *
17416 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATT-TCATCTAAAAAAGCTCCTTTCAGCA
1 AAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATTCTC-T-TAAAAAAGCTCATCTCAGCA
**** *
17480 AAGGCTCAACAACTTTAAAATTCTCAT-TTTTTTCAAATTTAAGTTCTCATCTT
64 AAGGCTCAACAACTTTAAAATTCTCATCTTGGAACAAATTTAAATTCTCATCTT
17533 TGAACAAGTA
Statistics
Matches: 103, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
119 14 0.14
120 46 0.45
121 43 0.42
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (119 bp):
AAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATTCTCTTAAAAAAGCTCATCTCAGCAAA
GGCTCAACAACTTTAAAATTCTCATCTTGGAACAAATTTAAATTCTCATCTTGA
Found at i:19245 original size:12 final size:12
Alignment explanation
Indices: 19225--19261 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
19215 GTTTCCAGTT
19225 TAATATTAATAA
1 TAATATTAATAA
*
19237 TAATTTTAATAA
1 TAATATTAATAA
19249 TAATATTAATAA
1 TAATATTAATAA
19261 T
1 T
19262 TAAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TAATATTAATAA
Found at i:19246 original size:18 final size:18
Alignment explanation
Indices: 19223--19258 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19213 TCGTTTCCAG
*
19223 TTTAATATTAATAATAAT
1 TTTAATAATAATAATAAT
*
19241 TTTAATAATAATATTAAT
1 TTTAATAATAATAATAAT
19259 AATTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAATAATAATAATAAT
Done.