Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168250.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_481, 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: 25357
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:407 original size:9 final size:9
Alignment explanation
Indices: 393--417 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
383 TCAGGTTATG
393 CACCATGTA
1 CACCATGTA
402 CACCATGTA
1 CACCATGTA
411 CACCATG
1 CACCATG
418 ATCGGGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.36, G:0.12, T:0.20
Consensus pattern (9 bp):
CACCATGTA
Found at i:3827 original size:45 final size:45
Alignment explanation
Indices: 3702--3832 Score: 113
Period size: 45 Copynumber: 2.9 Consensus size: 45
3692 TGTGGGTAGT
* * * * * * **
3702 TACCTTGAACATCATTGGCACATACTGGCCCTTAGTG-AGAGCAGT
1 TACCTCGAACACCATTGGCATATACTAGCCATTGGTGCA-AGCACA
*
3747 TACCTCGAACACCATTGGCATATACTAGGCATTGGTGCAAGCACA
1 TACCTCGAACACCATTGGCATATACTAGCCATTGGTGCAAGCACA
* * * *
3792 TACCTTGACCACCATTGGCATCTA-TAGACCCTTGGTGCAAG
1 TACCTCGAACACCATTGGCATATACTAG-CCATTGGTGCAAG
3833 ATTTGCTTGT
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
44 3 0.04
45 66 0.94
46 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (45 bp):
TACCTCGAACACCATTGGCATATACTAGCCATTGGTGCAAGCACA
Found at i:8975 original size:30 final size:30
Alignment explanation
Indices: 8939--8998 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
8929 AAGGATCCTT
8939 GAATGAGGTATAAGAGGTTCTCATGCAGTG
1 GAATGAGGTATAAGAGGTTCTCATGCAGTG
8969 GAATGAGGTATAAGAGGTTCTCATGCAGTG
1 GAATGAGGTATAAGAGGTTCTCATGCAGTG
8999 AAAGCATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.10, G:0.33, T:0.27
Consensus pattern (30 bp):
GAATGAGGTATAAGAGGTTCTCATGCAGTG
Found at i:14012 original size:9 final size:9
Alignment explanation
Indices: 13988--14017 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
13978 GACCTTTTTA
13988 TATTTTAAT
1 TATTTTAAT
13997 GTATTTTAAT
1 -TATTTTAAT
14007 TATTTTAAT
1 TATTTTAAT
14016 TA
1 TA
14018 ATAAAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:20867 original size:143 final size:144
Alignment explanation
Indices: 20608--20871 Score: 381
Period size: 143 Copynumber: 1.8 Consensus size: 144
20598 CTTATTCAAA
* * * * *
20608 ATAAAATAATACTATTTTATTAATATTCCTAAAATTAATGAGTAAGAGATTTAAAAAATGAATCT
1 ATAAAATAATACTAATTTATTAATATTCCAAAAATTAATAAGTAAGAAATTTAAAAAATAAATCT
*
20673 ATTTACCGTACAAGTTCAAATAGTTATAACTAATTGAACAATTATCTATTTCAAATCATTAAGAC
66 ATTTACCGAACAAGTTCAAATAGTTATAACTAATTGAACAATTATCTATTTCAAATCATTAAGAC
20738 CATTTGTTTTTGTC
131 CATTTGTTTTTGTC
* *
20752 ATAAAATAATA-TAAATTTATTAATATTTCAAAAATTACTAAGT-AGAAATTTAAAAAATAAATC
1 ATAAAATAATACT-AATTTATTAATATTCCAAAAATTAATAAGTAAGAAATTTAAAAAATAAATC
*** *
20815 TATTTTTTGAACACA-TTCAAATAGTTATAACTATTTGAACAATTATCTATTTCAAAT
65 TATTTACCGAACA-AGTTCAAATAGTTATAACTAATTGAACAATTATCTATTTCAAAT
20872 AGCTATGACA
Statistics
Matches: 106, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
143 69 0.65
144 37 0.35
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (144 bp):
ATAAAATAATACTAATTTATTAATATTCCAAAAATTAATAAGTAAGAAATTTAAAAAATAAATCT
ATTTACCGAACAAGTTCAAATAGTTATAACTAATTGAACAATTATCTATTTCAAATCATTAAGAC
CATTTGTTTTTGTC
Found at i:21486 original size:180 final size:180
Alignment explanation
Indices: 21300--21631 Score: 415
Period size: 180 Copynumber: 1.8 Consensus size: 180
21290 ACATATTTAG
*
21300 TTTTTAAATCTC-TTACTTATTAGTTTTT-GAAATATTAATAAATTAAAATTA-TGTTATTCCTA
1 TTTTTAAATC-CATTACTTATTAATTTTTAG-AATATTAATAAATTAAAATTACT-TTATTCC-A
* * * * ** *
21362 ATTA-G-TTGTATGAACAAAAACAATTGTTTTATGATGAAACAAAAGGTCATAA-TGATTTGAAA
62 AGTAGGATTATATCAACAAAAA-AATTGTTTTATAACAAAACAAAAGGTCATAACAG-TTTGAAA
*
21424 TAGATAATTGTTCAAACAATTATAACTATTTGTATTGGTCATGCCAATAGATTCAT
125 TAAATAATTGTTCAAACAATTATAACTATTTGTATTGGTCATGCCAATAGATTCAT
* **
21480 TTTTTAAATCCATTATTTATTAATTTTTAGAATATTAATAAATTAGCATTACTTTATTCCAAGTA
1 TTTTTAAATCCATTACTTATTAATTTTTAGAATATTAATAAATTAAAATTACTTTATTCCAAGTA
* * *
21545 GGATTATATCAACAGAAAATTTGTTTTATAACAAAACAAATGGTCATAACAGTTTGAAATAAATA
66 GGATTATATCAACAAAAAAATTGTTTTATAACAAAACAAAAGGTCATAACAGTTTGAAATAAATA
**
21610 ATTGTTCAAATTATTATAACTA
131 ATTGTTCAAACAATTATAACTA
21632 ATTGAACTAG
Statistics
Matches: 129, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
179 5 0.04
180 109 0.84
181 15 0.12
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (180 bp):
TTTTTAAATCCATTACTTATTAATTTTTAGAATATTAATAAATTAAAATTACTTTATTCCAAGTA
GGATTATATCAACAAAAAAATTGTTTTATAACAAAACAAAAGGTCATAACAGTTTGAAATAAATA
ATTGTTCAAACAATTATAACTATTTGTATTGGTCATGCCAATAGATTCAT
Done.