Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168024.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_278, 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: 39910
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
File 2 of 2
Found at i:35183 original size:12 final size:12
Alignment explanation
Indices: 35166--35197 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
35156 TATTTAAGTT
35166 ATAATTATTAAA
1 ATAATTATTAAA
*
35178 ATAATTAATAAA
1 ATAATTATTAAA
35190 ATAATTAT
1 ATAATTAT
35198 AATTTATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATAATTATTAAA
Found at i:36056 original size:31 final size:31
Alignment explanation
Indices: 36008--36078 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
35998 ATCAAATAAA
* **
36008 TATTAATAATTTAAATATTTTAATAATCAAT
1 TATTAATTATTTAAATATGATAATAATCAAT
* *
36039 TATTAATTA-TTATAATATGATAATATTTAAT
1 TATTAATTATTTA-AATATGATAATAATCAAT
36070 TA-TAATTAT
1 TATTAATTAT
36079 AATTAATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
30 9 0.27
31 24 0.73
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
TATTAATTATTTAAATATGATAATAATCAAT
Found at i:36210 original size:20 final size:20
Alignment explanation
Indices: 36185--36248 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
36175 AATTATATAT
*
36185 ATAATTTTTAAAAAATTTTA
1 ATAATTTTTAAAAAATTTAA
*
36205 ATAATTTTATAAATAATTTAA
1 ATAATTTT-TAAAAAATTTAA
36226 ATATTATTTTTATAAACAATTTA
1 ATA--ATTTTTA-AAA-AATTTA
36249 CAATTAGATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 8 0.22
21 13 0.36
22 2 0.06
23 7 0.19
24 6 0.17
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAATTTTTAAAAAATTTAA
Found at i:36881 original size:16 final size:18
Alignment explanation
Indices: 36836--36886 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
36826 ATTATTGAAA
*
36836 TAATA-ATTATAAAATATT
1 TAATATATTAT-AATTATT
*
36854 TAATATATTATAGTTATT
1 TAATATATTATAATTATT
36872 TAA-A-ATTATAATTAT
1 TAATATATTATAATTAT
36887 AATATAGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 10 0.34
17 1 0.03
18 13 0.45
19 5 0.17
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TAATATATTATAATTATT
Found at i:37190 original size:12 final size:13
Alignment explanation
Indices: 37173--37208 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
37163 TAGTATAATA
37173 TTATAATAA-ATT
1 TTATAATAATATT
37185 TTATAATAATATT
1 TTATAATAATATT
*
37198 TTATGATAATA
1 TTATAATAATA
37209 ATTATAGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
TTATAATAATATT
Found at i:37408 original size:24 final size:23
Alignment explanation
Indices: 37342--37408 Score: 57
Period size: 24 Copynumber: 2.8 Consensus size: 23
37332 TCATATAAAT
* *
37342 AATAATT-ATATATATAATTAGTA
1 AATAATTAATAT-TATAAATAATA
*
37365 ATTAAATTAATAATT-TAAATAATA
1 AAT-AATTAAT-ATTATAAATAATA
37389 AATAATTACATATTATAAAT
1 AATAATTA-ATATTATAAAT
37409 TGTATTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
23 10 0.29
24 20 0.57
25 3 0.09
26 2 0.06
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (23 bp):
AATAATTAATATTATAAATAATA
Found at i:37510 original size:18 final size:19
Alignment explanation
Indices: 37477--37512 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
37467 AGTTAATTGA
*
37477 CTTGTTCTAATAAATTAAG
1 CTTGTACTAATAAATTAAG
37496 CTTGTACTAAT-AATTAA
1 CTTGTACTAATAAATTAA
37513 TAGTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (19 bp):
CTTGTACTAATAAATTAAG
Found at i:37626 original size:23 final size:23
Alignment explanation
Indices: 37575--37627 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
37565 TAAATCTCTA
* *
37575 TAAATAA-TATTATTTATATTAT
1 TAAATAATTATTATATATATAAT
**
37597 TTGATAATTATTATATATATAAT
1 TAAATAATTATTATATATATAAT
37620 TAAATAAT
1 TAAATAAT
37628 AAATAAGTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TAAATAATTATTATATATATAAT
Found at i:37983 original size:41 final size:44
Alignment explanation
Indices: 37936--38032 Score: 114
Period size: 39 Copynumber: 2.3 Consensus size: 44
37926 ATTATAAACA
*
37936 TAATTTATATTAAAATAATTAATAAA-TTATATCAAC-ATTATC
1 TAATTTATATTAAAATAAATAATAAACTTATATCAACAATTATC
* * *
37978 T-ATTTA-A-TAAATTAAATAATAAACTTATTTGAACAATTATC
1 TAATTTATATTAAAATAAATAATAAACTTATATCAACAATTATC
*
38019 TAATTAATATTAAA
1 TAATTTATATTAAA
38033 TTATTGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
39 14 0.31
40 9 0.20
41 12 0.27
42 5 0.11
43 1 0.02
44 4 0.09
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (44 bp):
TAATTTATATTAAAATAAATAATAAACTTATATCAACAATTATC
Found at i:38044 original size:29 final size:33
Alignment explanation
Indices: 37987--38046 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
37977 CTATTTAATA
37987 AATTAAATAATAAACTTATTTGAACAATTATCT
1 AATTAAATAATAAACTTATTTGAACAATTATCT
*
38020 AATT-AATATTAAA-TTA-TTGAA-AATTAT
1 AATTAAATAATAAACTTATTTGAACAATTAT
38047 TTATTATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 6 0.23
30 5 0.19
31 3 0.12
32 8 0.31
33 4 0.15
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (33 bp):
AATTAAATAATAAACTTATTTGAACAATTATCT
Found at i:38047 original size:41 final size:39
Alignment explanation
Indices: 37936--38048 Score: 93
Period size: 41 Copynumber: 2.7 Consensus size: 39
37926 ATTATAAACA
* * *
37936 TAATTTATATTAAAATAATTAATAAATTATATCAACATTATC
1 TAATTAATATT-AAATTATT-A-AAATTATTTCAACATTATC
* * * *
37978 TATTTAATAAATTAAA-TAATAAACTTATTTGAACAATTATC
1 TAATTAAT--ATTAAATTATTAAAATTATTTCAAC-ATTATC
38019 TAATTAATATTAAATTATTGAAAATTATTT
1 TAATTAATATTAAATTATT-AAAATTATTT
38049 ATTATAGTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
39 6 0.11
40 13 0.23
41 23 0.41
42 8 0.14
43 3 0.05
44 3 0.05
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (39 bp):
TAATTAATATTAAATTATTAAAATTATTTCAACATTATC
Found at i:38385 original size:18 final size:18
Alignment explanation
Indices: 38339--38385 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
38329 TATTATTTAA
*
38339 TAAT-ATTAAAAATAAAT
1 TAATAATTAAAATTAAAT
38356 TAATAATT-AAATTAATAT
1 TAATAATTAAAATTAA-AT
38374 TAA-AATTAAAAT
1 TAATAATTAAAAT
38386 CCTTATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAATAATTAAAATTAAAT
Found at i:39140 original size:17 final size:18
Alignment explanation
Indices: 39074--39137 Score: 71
Period size: 17 Copynumber: 3.6 Consensus size: 18
39064 TTTAATATTA
*
39074 TTATATAATACTTTATAT
1 TTATATAATACTTAATAT
39092 TTATA-AATAGTCTATAATAT
1 TTATATAATA--CT-TAATAT
39112 TT-TATAATA-TTAATAT
1 TTATATAATACTTAATAT
39128 TTATATAATA
1 TTATATAATA
39138 TTATTCAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
16 8 0.20
17 12 0.30
18 5 0.12
19 4 0.10
20 11 0.28
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATATAATACTTAATAT
Found at i:39141 original size:10 final size:10
Alignment explanation
Indices: 39072--39141 Score: 55
Period size: 10 Copynumber: 7.6 Consensus size: 10
39062 TATTTAATAT
39072 TATTATATAA
1 TATTATATAA
39082 TACTT-TAT-A
1 TA-TTATATAA
39091 T-TTATA-AA
1 TATTATATAA
* *
39099 TAGTCTATAA
1 TATTATATAA
*
39109 TATTTTATAA
1 TATTATATAA
39119 TATTA-AT-A
1 TATTATATAA
39127 T-TTATATAA
1 TATTATATAA
39136 TATTAT
1 TATTAT
39142 TCAAAAGTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 16
0.69 0.07 0.24
Matches are distributed among these distances:
7 5 0.11
8 8 0.17
9 9 0.19
10 23 0.49
11 2 0.04
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (10 bp):
TATTATATAA
Found at i:39803 original size:15 final size:14
Alignment explanation
Indices: 39775--39820 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
39765 TTATTTATAT
*
39775 TTAATTCTTAAATA
1 TTAATTATTAAATA
*
39789 TTAATTAATTTAATA
1 TTAATT-ATTAAATA
*
39804 TGAATTATTAAATA
1 TTAATTATTAAATA
39818 TTA
1 TTA
39821 TCATTATTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (14 bp):
TTAATTATTAAATA
Done.