Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168290.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_517, 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: 24233
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Found at i:1218 original size:36 final size:37
Alignment explanation
Indices: 1151--1230 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 37
1141 GGTGTGGCTC
1151 CAGGAGCAGTCACCCCACCAACGGCTTGAGGATGTCT
1 CAGGAGCAGTCACCCCACCAACGGCTTGAGGATGTCT
* *
1188 CAGGAGCAGTCGCCCCA-CTACGGCTTGAGGATGTCT
1 CAGGAGCAGTCACCCCACCAACGGCTTGAGGATGTCT
1224 CAGGAGC
1 CAGGAGC
1231 CTCATCAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 25 0.61
37 16 0.39
ACGTcount: A:0.23, C:0.31, G:0.30, T:0.16
Consensus pattern (37 bp):
CAGGAGCAGTCACCCCACCAACGGCTTGAGGATGTCT
Found at i:1861 original size:33 final size:34
Alignment explanation
Indices: 1795--1864 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
1785 TTTTTTCTGG
**
1795 CAATATACTCATACGCCACAAAGGGAAACAAAGT
1 CAATATACTCATACGCCACAAAAAGAAACAAAGT
*
1829 CAATATGCTCATACGCCA-AAAAAGAAACAAAGT
1 CAATATACTCATACGCCACAAAAAGAAACAAAGT
1862 CAA
1 CAA
1865 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:3438 original size:20 final size:20
Alignment explanation
Indices: 3413--3459 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3403 CATTTACAGA
*
3413 TAAATATAAAATCTGTGTAT
1 TAAATATAAAATATGTGTAT
* *
3433 TAAATATAGACTATGTGTAT
1 TAAATATAAAATATGTGTAT
3453 TAAATAT
1 TAAATAT
3460 CATTTTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (20 bp):
TAAATATAAAATATGTGTAT
Found at i:7095 original size:3 final size:3
Alignment explanation
Indices: 7081--7117 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
7071 AAGTGATGAC
*
7081 ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
7118 ACAAGAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:7670 original size:17 final size:17
Alignment explanation
Indices: 7648--7687 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
7638 CCTATACGTC
7648 AGTTTGACGATTTTTTT
1 AGTTTGACGATTTTTTT
7665 AGTTTGACGATTTTTTT
1 AGTTTGACGATTTTTTT
7682 AGTTTG
1 AGTTTG
7688 GTTCTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.05, G:0.20, T:0.57
Consensus pattern (17 bp):
AGTTTGACGATTTTTTT
Found at i:13659 original size:24 final size:23
Alignment explanation
Indices: 13603--13659 Score: 55
Period size: 24 Copynumber: 2.4 Consensus size: 23
13593 AAATTTTCAA
13603 CAAATAACTTGTCCCTTTTATTGG
1 CAAATAACTTGTCCCTTTTA-TGG
* *
13627 CCAAT-ACTTGTCCCCTCTTTA-GT
1 CAAATAACTTGT-CCCT-TTTATGG
13650 CAAATAACTT
1 CAAATAACTT
13660 TAAGATTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
23 11 0.41
24 12 0.44
25 4 0.15
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.39
Consensus pattern (23 bp):
CAAATAACTTGTCCCTTTTATGG
Found at i:19614 original size:21 final size:21
Alignment explanation
Indices: 19584--19632 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
19574 TAAAAGATAT
* *
19584 AAATTTTTA-TATTTATTTTAG
1 AAATTGTTATTATTTA-TTAAG
19605 AAATTGTTATTTATTTATTAAG
1 AAATTGTTA-TTATTTATTAAG
19627 AAATTG
1 AAATTG
19633 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:19896 original size:19 final size:19
Alignment explanation
Indices: 19872--19908 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19862 TATATAAAGA
*
19872 TATAAAAGTTAAAATATTT
1 TATAAAAATTAAAATATTT
19891 TATAAAAATTAAAATATT
1 TATAAAAATTAAAATATT
19909 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.