Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168106.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_351, 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: 32033
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:1341 original size:4 final size:4
Alignment explanation
Indices: 1327--1357 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
1317 GCAAACATTT
1327 ATTA GATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA -ATTA ATTA ATTA ATTA ATTA ATTA AT
1358 AGGGAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:4202 original size:61 final size:60
Alignment explanation
Indices: 4102--4215 Score: 183
Period size: 61 Copynumber: 1.9 Consensus size: 60
4092 CTATTTGCTT
*
4102 ATGTATTTTCATTTAATCTGGTTGTAATGGAGTGGTTATTTTCCTAAACAGTTGTCTGAA
1 ATGTATTTTCATTTAATCTGGTTGTAATGGAGTGGTTATTTTACTAAACAGTTGTCTGAA
* * *
4162 ATGTACTTTTCATTTAATCTGGTTTTGATGGAGTGGTTATTTTACTAAGCAGTT
1 ATGTA-TTTTCATTTAATCTGGTTGTAATGGAGTGGTTATTTTACTAAACAGTT
4216 TTTTTAATGA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 5 0.10
61 44 0.90
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (60 bp):
ATGTATTTTCATTTAATCTGGTTGTAATGGAGTGGTTATTTTACTAAACAGTTGTCTGAA
Found at i:12022 original size:21 final size:20
Alignment explanation
Indices: 11984--12026 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
11974 CAATCATCCC
*
11984 ATAAATTAAAATATAATTAA
1 ATAAATTAAAATAAAATTAA
*
12004 ATAAATTTAACATAAAATTAA
1 ATAAA-TTAAAATAAAATTAA
12025 AT
1 AT
12027 CAAAAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAAATTAAAATAAAATTAA
Found at i:12267 original size:19 final size:19
Alignment explanation
Indices: 12232--12270 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
12222 ATTTATTGTT
12232 AAATTTTTTTTACCAAAAAA
1 AAATTTTTTTTA-CAAAAAA
12252 AAATTTTTTATT-CAAAAAA
1 AAATTTTTT-TTACAAAAAA
12271 TTTTAAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 9 0.50
21 2 0.11
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATTTTTTTTACAAAAAA
Found at i:13179 original size:22 final size:22
Alignment explanation
Indices: 13129--13179 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
13119 TTTGTTTTCC
13129 AATTTTTTGAGTGCTCATAAGA
1 AATTTTTTGAGTGCTCATAAGA
*
13151 AA-ATTTTGAAGTG-TCCA-AAGA
1 AATTTTTTG-AGTGCT-CATAAGA
13172 AATTTTTT
1 AATTTTTT
13180 TTTTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (22 bp):
AATTTTTTGAGTGCTCATAAGA
Found at i:13544 original size:22 final size:23
Alignment explanation
Indices: 13511--13559 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
13501 ATATATTAAT
*
13511 TTTA-ATTAATTTAA-AATAATAA
1 TTTATATTAATTTAATAA-AAAAA
13533 TTTATATT-ATTTAATAAAAAAA
1 TTTATATTAATTTAATAAAAAAA
13555 TTTAT
1 TTTAT
13560 CTACTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTATATTAATTTAATAAAAAAA
Found at i:13546 original size:27 final size:28
Alignment explanation
Indices: 13492--13555 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
13482 TTATATATTT
*
13492 TTTAAAAAAATATATTAATTTTAATTAA
1 TTTAAAAAAATATATTAATATTAATTAA
* * *
13520 TTTAAAATAATA-ATTTATATTATTTAA
1 TTTAAAAAAATATATTAATATTAATTAA
13547 --TAAAAAAAT
1 TTTAAAAAAAT
13556 TTATCTACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 8 0.26
27 12 0.39
28 11 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
TTTAAAAAAATATATTAATATTAATTAA
Found at i:16779 original size:22 final size:23
Alignment explanation
Indices: 16754--16803 Score: 93
Period size: 22 Copynumber: 2.2 Consensus size: 23
16744 TTCGAAATTA
16754 ATAAAATATTATTTTTTAAA-AT
1 ATAAAATATTATTTTTTAAATAT
16776 ATAAAATATTATTTTTTAAATAT
1 ATAAAATATTATTTTTTAAATAT
16799 ATAAA
1 ATAAA
16804 TAATTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAAAATATTATTTTTTAAATAT
Found at i:16809 original size:23 final size:22
Alignment explanation
Indices: 16753--16809 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
16743 ATTCGAAATT
16753 AATA-AAAT-ATTATTTTTTAA
1 AATATAAATAATTATTTTTTAA
16773 AATATAAA-ATATTATTTTTTAA
1 AATATAAATA-ATTATTTTTTAA
16795 ATATATAAATAATTA
1 A-ATATAAATAATTA
16810 AAAAATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.12
21 3 0.09
22 13 0.41
23 11 0.34
24 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATAAATAATTATTTTTTAA
Found at i:22114 original size:2 final size:2
Alignment explanation
Indices: 22107--22132 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22097 ACAATCTCAA
22107 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
22133 TTATAAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:29634 original size:21 final size:21
Alignment explanation
Indices: 29609--29651 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
29599 ATTGTTTCTA
29609 ACTATGATATCCTTTGTTATC
1 ACTATGATATCCTTTGTTATC
29630 ACTATGATATCCTTTGTTATC
1 ACTATGATATCCTTTGTTATC
29651 A
1 A
29652 AATGCGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.47
Consensus pattern (21 bp):
ACTATGATATCCTTTGTTATC
Found at i:29770 original size:2 final size:2
Alignment explanation
Indices: 29763--29792 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29753 TATGTGAAAG
29763 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29793 TTTTATGTTT
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):
AT
Found at i:30886 original size:18 final size:18
Alignment explanation
Indices: 30851--30884 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30841 ATATATATTT
*
30851 TTTATCTTTTTTATTTTA
1 TTTATCTTTTGTATTTTA
30869 TTTAT-TTTTGTATTTT
1 TTTATCTTTTGTATTTT
30885 TACTTATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTATCTTTTGTATTTTA
Found at i:31363 original size:31 final size:31
Alignment explanation
Indices: 31328--31388 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
31318 TTCCGGCGAC
* *
31328 AATTCCGGCGAAGTTTGAATTTTTCGACGAA
1 AATTCCGACCAAGTTTGAATTTTTCGACGAA
*
31359 AATTCCGACCAATTTTGAATTTTTCGACGA
1 AATTCCGACCAAGTTTGAATTTTTCGACGA
31389 CCAACCCAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (31 bp):
AATTCCGACCAAGTTTGAATTTTTCGACGAA
Found at i:31732 original size:10 final size:10
Alignment explanation
Indices: 31717--31748 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
31707 CCAGCCCCCT
31717 CCGAGTCGAG
1 CCGAGTCGAG
31727 CCGAGTCGAG
1 CCGAGTCGAG
31737 CCGAGTCGAG
1 CCGAGTCGAG
31747 CC
1 CC
31749 AAGCTACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.19, C:0.34, G:0.38, T:0.09
Consensus pattern (10 bp):
CCGAGTCGAG
Found at i:31913 original size:10 final size:10
Alignment explanation
Indices: 31898--31922 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
31888 TGTAATATTC
31898 TTTTTATTTA
1 TTTTTATTTA
31908 TTTTTATTTA
1 TTTTTATTTA
31918 TTTTT
1 TTTTT
31923 TTATTATTCT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTATTTA
Done.