Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168245.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_477, 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: 25537
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4060 original size:22 final size:24
Alignment explanation
Indices: 4015--4061 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
4005 AAATAATAAT
*
4015 AAAATATAAAAATATAAAAGGCAA
1 AAAATATAAAAATATAAAACGCAA
*
4039 AAAAT-TAAAAA-ATTAAACGCAA
1 AAAATATAAAAATATAAAACGCAA
4061 A
1 A
4062 TCTAAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 6 0.29
24 5 0.24
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.17
Consensus pattern (24 bp):
AAAATATAAAAATATAAAACGCAA
Found at i:4109 original size:43 final size:43
Alignment explanation
Indices: 4059--4143 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
4049 AATTAAACGC
*
4059 AAATCTAAATCATCATAAAAAAATTTAGTCGTATTTTTCTTTT
1 AAATCTAAATCATCATAAAAAAATTTAGTCGCATTTTTCTTTT
4102 AAATCTAAATCATCATAAAAAAATTTAGTCGCATTTTTCTTT
1 AAATCTAAATCATCATAAAAAAATTTAGTCGCATTTTTCTTT
4144 CTCTTTTTCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.42
Consensus pattern (43 bp):
AAATCTAAATCATCATAAAAAAATTTAGTCGCATTTTTCTTTT
Found at i:10502 original size:18 final size:17
Alignment explanation
Indices: 10454--10501 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
10444 CTTCCCTAAA
*
10454 TTTTTTGTAATTTTATT
1 TTTTTTTTAATTTTATT
* *
10471 TTTTTCTAAATTTTCATT
1 TTTTTTTTAATTTT-ATT
10489 TTTTTTTT-ATTTT
1 TTTTTTTTAATTTT
10502 TTCTGTTTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTTTTTAATTTTATT
Found at i:10745 original size:22 final size:22
Alignment explanation
Indices: 10717--10760 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
10707 ACAATTGTAG
*
10717 AATTTAAATGGACCATATATGC
1 AATTTAAATGGACCATAAATGC
10739 AATTTAAATGGACCATAAATGC
1 AATTTAAATGGACCATAAATGC
10761 TTCCCGTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (22 bp):
AATTTAAATGGACCATAAATGC
Found at i:20816 original size:35 final size:35
Alignment explanation
Indices: 20770--20842 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
20760 ATACTATTAG
20770 GTTCTGGCGTTTCCTCCAACTCATCTGTTCCGCCA
1 GTTCTGGCGTTTCCTCCAACTCATCTGTTCCGCCA
20805 GTTCTGGCGTTTCCTCCAACTCATCTGTTCCGCCA
1 GTTCTGGCGTTTCCTCCAACTCATCTGTTCCGCCA
20840 GTT
1 GTT
20843 TTAAGTAGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.11, C:0.36, G:0.18, T:0.36
Consensus pattern (35 bp):
GTTCTGGCGTTTCCTCCAACTCATCTGTTCCGCCA
Found at i:24797 original size:28 final size:28
Alignment explanation
Indices: 24740--24800 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
24730 TTTAATTCAC
* * *
24740 ATATATATATAAATTAAAATATATATTT
1 ATATATATAAAAATTAAAATATAAAATT
*
24768 ATATTTATAAAAATTAAAA-ATAAAAATT
1 ATATATATAAAAATTAAAATAT-AAAATT
24796 ATATA
1 ATATA
24801 AAAGTAACAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
ATATATATAAAAATTAAAATATAAAATT
Done.