Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168239.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_471, 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: 25715
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Found at i:3769 original size:36 final size:36
Alignment explanation
Indices: 3717--3795 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
3707 GGTGTGGCTC
3717 CAGGAGCAGTCACCCCACCACGGCTTGAGGATGTCT
1 CAGGAGCAGTCACCCCACCACGGCTTGAGGATGTCT
* *
3753 CAGGAGCAGTCGCCCCACTACGGCTTGAGGATGTCT
1 CAGGAGCAGTCACCCCACCACGGCTTGAGGATGTCT
3789 CAGGAGC
1 CAGGAGC
3796 CTCATCAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.22, C:0.32, G:0.30, T:0.16
Consensus pattern (36 bp):
CAGGAGCAGTCACCCCACCACGGCTTGAGGATGTCT
Found at i:4424 original size:33 final size:34
Alignment explanation
Indices: 4358--4427 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
4348 TTTTTTCTGG
**
4358 CAATATACTCATACGCCACAAAGGGAAACAAAGT
1 CAATATACTCATACGCCACAAAAAGAAACAAAGT
*
4392 CAATATGCTCATACGCCA-AAAAAGAAACAAAGT
1 CAATATACTCATACGCCACAAAAAGAAACAAAGT
4425 CAA
1 CAA
4428 GGCACCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 16 0.48
34 17 0.52
ACGTcount: A:0.50, C:0.23, G:0.13, T:0.14
Consensus pattern (34 bp):
CAATATACTCATACGCCACAAAAAGAAACAAAGT
Found at i:9277 original size:20 final size:20
Alignment explanation
Indices: 9239--9292 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
9229 TATAAATTTT
9239 TTAAA-ATTATATT-TATAA
1 TTAAATATTATATTATATAA
*
9257 TTAAATATTATTTTATATAA
1 TTAAATATTATATTATATAA
*
9277 TTAACTATTATATTAT
1 TTAAATATTATATTAT
9293 CGATTAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 5 0.16
19 7 0.23
20 19 0.61
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAAATATTATATTATATAA
Found at i:9852 original size:15 final size:17
Alignment explanation
Indices: 9832--9863 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
9822 TTAATTATTA
9832 ATTTTA-ATAAA-TTTT
1 ATTTTACATAAACTTTT
9847 ATTTTACATAAACTTTT
1 ATTTTACATAAACTTTT
9864 TATTAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTACATAAACTTTT
Found at i:9892 original size:24 final size:23
Alignment explanation
Indices: 9860--9916 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 23
9850 TTACATAAAC
9860 TTTTTATTAAAATTATAATAATT
1 TTTTTATTAAAATTATAATAATT
*
9883 TTTTTAATTATAATTATAATAATT
1 TTTTT-ATTAAAATTATAATAATT
*
9907 ATTATTATTA
1 -TTTTTATTA
9917 TTTTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 5 0.17
24 21 0.70
25 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTTATTAAAATTATAATAATT
Found at i:16543 original size:23 final size:23
Alignment explanation
Indices: 16488--16543 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
16478 AAATTTTCAA
16488 CAAATAACTTGTCCCTTTTATTGG
1 CAAATAACTTGTCCCTTTTA-TGG
* *
16512 CCAAT-ACTTGTCCCTCTTTA-GT
1 CAAATAACTTGTCCCT-TTTATGG
16534 CAAATAACTT
1 CAAATAACTT
16544 TAAGATTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 5 0.19
23 14 0.52
24 8 0.30
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (23 bp):
CAAATAACTTGTCCCTTTTATGG
Found at i:22511 original size:21 final size:21
Alignment explanation
Indices: 22481--22529 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
22471 TAAAAGATAT
* *
22481 AAATTTTTA-TATTTATTTTAG
1 AAATTGTTATTATTTA-TTAAG
22502 AAATTGTTATTTATTTATTAAG
1 AAATTGTTA-TTATTTATTAAG
22524 AAATTG
1 AAATTG
22530 ACTTCATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 10 0.42
23 6 0.25
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (21 bp):
AAATTGTTATTATTTATTAAG
Found at i:22791 original size:19 final size:19
Alignment explanation
Indices: 22767--22803 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
22757 TATATAAAGA
*
22767 TATAAAAGTTAAAATATTT
1 TATAAAAATTAAAATATTT
22786 TATAAAAATTAAAATATT
1 TATAAAAATTAAAATATT
22804 CAATGTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
TATAAAAATTAAAATATTT
Done.