Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168318.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_542, 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: 23577
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:1288 original size:14 final size:14
Alignment explanation
Indices: 1269--1296 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1259 CCGATATCCT
1269 GCATTATGAAAACA
1 GCATTATGAAAACA
1283 GCATTATGAAAACA
1 GCATTATGAAAACA
1297 TTACAACAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
GCATTATGAAAACA
Found at i:7659 original size:13 final size:13
Alignment explanation
Indices: 7641--7666 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7631 ATATAATTAT
7641 AATATAAAAATAA
1 AATATAAAAATAA
7654 AATATAAAAATAA
1 AATATAAAAATAA
7667 TATGACTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AATATAAAAATAA
Found at i:7874 original size:13 final size:12
Alignment explanation
Indices: 7858--7887 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
7848 TTAAATTGAG
7858 TTTTTATTTTTA
1 TTTTTATTTTTA
7870 TTTTTATTTTTTA
1 TTTTTA-TTTTTA
7883 TTTTT
1 TTTTT
7888 TAATAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTATTTTTA
Found at i:7889 original size:7 final size:6
Alignment explanation
Indices: 7858--7887 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
7848 TTAAATTGAG
7858 TTTTTA TTTTTA TTTTTA TTTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA -TTTTTA TTTTT
7888 TAATAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTA
Found at i:8303 original size:17 final size:19
Alignment explanation
Indices: 8263--8298 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8253 GAATCAAATT
*
8263 ATATATTTTTATTAATTTG
1 ATATATTTTTATAAATTTG
8282 ATATATTTTTA-AAATTT
1 ATATATTTTTATAAATTT
8299 TTATAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
ATATATTTTTATAAATTTG
Found at i:17127 original size:21 final size:22
Alignment explanation
Indices: 17103--17145 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
17093 TATATATTTA
17103 TATTTGTATTCC-TAG-ATTAAG
1 TATTTGTA-TCCTTAGAATTAAG
17124 TATTTGTATCCTTAGAATTAAG
1 TATTTGTATCCTTAGAATTAAG
17146 AACAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 3 0.15
21 11 0.55
22 6 0.30
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (22 bp):
TATTTGTATCCTTAGAATTAAG
Found at i:17319 original size:24 final size:26
Alignment explanation
Indices: 17291--17341 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
17281 ATACATTTAA
17291 TTTTA-CTCTTAATTTTTC-ATATAG
1 TTTTATCTCTTAATTTTTCTATATAG
* *
17315 TTTTATTTTTTAATTTTTCTATATAG
1 TTTTATCTCTTAATTTTTCTATATAG
17341 T
1 T
17342 ATCAGAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 5 0.22
25 11 0.48
26 7 0.30
ACGTcount: A:0.24, C:0.08, G:0.04, T:0.65
Consensus pattern (26 bp):
TTTTATCTCTTAATTTTTCTATATAG
Found at i:18888 original size:22 final size:24
Alignment explanation
Indices: 18860--18903 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
18850 ATTATTTTTT
18860 AATATAAATATA-AAAT-TAAATA
1 AATATAAATATATAAATATAAATA
18882 AATATAAATATATAAATATAAA
1 AATATAAATATATAAATATAAA
18904 ATTAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 12 0.60
23 4 0.20
24 4 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
AATATAAATATATAAATATAAATA
Found at i:18898 original size:14 final size:15
Alignment explanation
Indices: 18861--18903 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
18851 TTATTTTTTA
18861 ATATAAATATAAAATT
1 ATATAAATAT-AAATT
*
18877 AAATAAATATAAA-T
1 ATATAAATATAAATT
18891 ATATAAATATAAA
1 ATATAAATATAAA
18904 ATTAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
15 3 0.12
16 9 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATATAAATATAAATT
Done.