Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167981.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_239, 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: 44689
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
File 2 of 2
Found at i:43302 original size:10 final size:10
Alignment explanation
Indices: 43266--43313 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
43256 CTTTATAAAA
43266 TAATATTTAT
1 TAATATTTAT
* *
43276 TAATTTATTAA
1 TAATAT-TTAT
43287 TAATATTTAT
1 TAATATTTAT
*
43297 TAATATTAAT
1 TAATATTTAT
43307 T-ATATTT
1 TAATATTT
43314 TATTTGTTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
9 5 0.16
10 18 0.58
11 8 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TAATATTTAT
Found at i:43433 original size:36 final size:38
Alignment explanation
Indices: 43380--43456 Score: 97
Period size: 36 Copynumber: 2.1 Consensus size: 38
43370 AAATCTAGTA
43380 ATATAAATATATTATATTATTAATT-TAAATATTAA-T
1 ATATAAATATATTATATTATTAATTGTAAATATTAACT
* * *
43416 ATATTAATA-ATTAATATTATTATTTGTCAATATTAACT
1 ATATAAATATATT-ATATTATTAATTGTAAATATTAACT
43454 ATA
1 ATA
43457 ATAGTTGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 3 0.09
36 19 0.54
37 9 0.26
38 4 0.11
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (38 bp):
ATATAAATATATTATATTATTAATTGTAAATATTAACT
Found at i:43703 original size:29 final size:30
Alignment explanation
Indices: 43626--43731 Score: 84
Period size: 29 Copynumber: 3.8 Consensus size: 30
43616 TATTATGATA
* * **
43626 ATAATTAAT-TATTATTAATTAAT-ATTTT
1 ATAATTAATATATTATAAATTATTAATAAT
43654 ATAATT--TATATTATAAATTATT-A-AAT
1 ATAATTAATATATTATAAATTATTAATAAT
* *
43680 ATAATATAATATATTATGATTTATTAATAAT
1 ATAAT-TAATATATTATAAATTATTAATAAT
*
43711 ATAATTAAAATATT-T-AATTAT
1 ATAATTAATATATTATAAATTAT
43732 AATTAGTTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
26 7 0.11
27 14 0.22
28 11 0.17
29 15 0.23
30 9 0.14
31 8 0.12
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
ATAATTAATATATTATAAATTATTAATAAT
Found at i:43718 original size:41 final size:41
Alignment explanation
Indices: 43605--43719 Score: 104
Period size: 41 Copynumber: 3.0 Consensus size: 41
43595 TATGACTAGA
*
43605 ATAATATAATATATTATG----A-TAATAAT-TAATT-ATT
1 ATAATATAATATATTATGATTTATTAATAATATAATTAAAT
* * * *
43639 ATTAAT-TAATATTTTATAATTTATATTATAA-ATTATTAAAT
1 A-TAATATAATATATTATGATTTAT-TAATAATATAATTAAAT
43680 ATAATATAATATATTATGATTTATTAATAATATAATTAAA
1 ATAATATAATATATTATGATTTATTAATAATATAATTAAA
43720 ATATTTAATT
Statistics
Matches: 61, Mismatches: 9, Indels: 15
0.72 0.11 0.18
Matches are distributed among these distances:
34 11 0.18
35 4 0.07
38 1 0.02
40 18 0.30
41 27 0.44
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.49
Consensus pattern (41 bp):
ATAATATAATATATTATGATTTATTAATAATATAATTAAAT
Found at i:43746 original size:16 final size:16
Alignment explanation
Indices: 43725--43755 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
43715 TTAAAATATT
43725 TAATTATAATTAGTTA
1 TAATTATAATTAGTTA
43741 TAATTATAATTAGTT
1 TAATTATAATTAGTT
43756 TTATGAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
TAATTATAATTAGTTA
Found at i:43872 original size:24 final size:24
Alignment explanation
Indices: 43825--43873 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
43815 ATAATTAACA
43825 ATATTATAATTTAATAATATATTT
1 ATATTATAATTTAATAATATATTT
* *
43849 ATATTATTTATTTAATATTA-ATTT
1 ATATTA-TAATTTAATAATATATTT
43873 A
1 A
43874 AAACAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATTATAATTTAATAATATATTT
Found at i:44036 original size:17 final size:17
Alignment explanation
Indices: 44016--44048 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
44006 ATAATTAATT
44016 AATAATATTA-ATAAATA
1 AATAAT-TTATATAAATA
44033 AATAATTTATATAAAT
1 AATAATTTATATAAAT
44049 TATTTGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATAATTTATATAAATA
Found at i:44224 original size:20 final size:20
Alignment explanation
Indices: 44199--44237 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
44189 AAATTTAATT
44199 TATAATAC-TTCATATTATTG
1 TATAATACTTTCA-ATTATTG
*
44219 TATAATTCTTTCAATTATT
1 TATAATACTTTCAATTATT
44238 AAAATGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.54
Consensus pattern (20 bp):
TATAATACTTTCAATTATTG
Found at i:44374 original size:22 final size:23
Alignment explanation
Indices: 44346--44404 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
44336 AATTATTCAA
*
44346 ATATTTAATT-TAATCAGTTATT
1 ATATTTAATTATAATAAGTTATT
*
44368 ATATTTAATTACTAGTAAGTTATT
1 ATATTTAATTA-TAATAAGTTATT
44392 ATA--TAATTATAAT
1 ATATTTAATTATAAT
44405 TATATAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 3 0.09
22 16 0.50
24 13 0.41
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (23 bp):
ATATTTAATTATAATAAGTTATT
Found at i:44635 original size:16 final size:17
Alignment explanation
Indices: 44610--44649 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
44600 ATTTTTATTA
*
44610 TAAA-TATATA-ATCAT
1 TAAATTATATATATAAT
44625 TAAATTATATATATAAT
1 TAAATTATATATATAAT
44642 T-AATTATA
1 TAAATTATA
44650 AATAAAGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 13 0.59
17 5 0.23
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATTATATATATAAT
Done.