Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168268.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_498, 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: 24860
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Found at i:928 original size:11 final size:11
Alignment explanation
Indices: 912--949 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
902 GTTATAATTA
912 AAATTTATATG
1 AAATTTATATG
*
923 AAATTTATA-A
1 AAATTTATATG
933 AAATTTTATATG
1 AAA-TTTATATG
945 AAATT
1 AAATT
950 CACATTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 3 0.13
11 17 0.74
12 3 0.13
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (11 bp):
AAATTTATATG
Found at i:1388 original size:10 final size:10
Alignment explanation
Indices: 1369--1409 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
1359 ATATAAAAAA
1369 ATTT-TATAT
1 ATTTATATAT
1378 ATTTATATAT
1 ATTTATATAT
1388 ATTTATATA-
1 ATTTATATAT
*
1397 AATTATA-AT
1 ATTTATATAT
1406 ATTT
1 ATTT
1410 CAATTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 1 0.04
9 13 0.46
10 14 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTTATATAT
Found at i:1394 original size:18 final size:18
Alignment explanation
Indices: 1371--1409 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1361 ATAAAAAAAT
*
1371 TTTATAT-ATTTATATATA
1 TTTATATAAATTATA-ATA
1389 TTTATATAAATTATAATA
1 TTTATATAAATTATAATA
1407 TTT
1 TTT
1410 CAATTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTATATAAATTATAATA
Found at i:4618 original size:24 final size:24
Alignment explanation
Indices: 4546--4618 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 24
4536 TACTTATTTC
* *
4546 AATTAAATTTGTTATTAAAATGTTAA
1 AATTAAATTT-TAATTAAAAT-ATAA
* *
4572 AA--ATATTTTATATTAATATTATAA
1 AATTAAATTTTA-ATTAA-AATATAA
4596 AATTAAATTTTAATTAAAATATA
1 AATTAAATTTTAATTAAAATATA
4619 TTATTTATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
23 1 0.03
24 20 0.54
25 7 0.19
26 9 0.24
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (24 bp):
AATTAAATTTTAATTAAAATATAA
Found at i:7357 original size:30 final size:30
Alignment explanation
Indices: 7321--7384 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
7311 AAATCTTAAC
7321 TCATGTTTCAAAATGATATAACAAATAAGT
1 TCATGTTTCAAAATGATATAACAAATAAGT
7351 TCATGTTTCAAAATGATATAACAAATAAGT
1 TCATGTTTCAAAATGATATAACAAATAAGT
7381 TCAT
1 TCAT
7385 ATGTTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (30 bp):
TCATGTTTCAAAATGATATAACAAATAAGT
Found at i:12635 original size:129 final size:128
Alignment explanation
Indices: 12364--12709 Score: 349
Period size: 129 Copynumber: 2.7 Consensus size: 128
12354 CTTTTATGAG
* * * ***
12364 TACTTCATAAGAAGTTAACATGT-AACATTTTGTTTCAAAATTACTATAATACTTTTATTAAATT
1 TACTTCATAAAAATTTGACATGTGAA-ATTTTGTTT-AAAATTACTATAATACCACTATTAAATT
* * * * * *
12428 ATATATTAATTTTTAACATAATATAAAATTAACCACATATTAAATTATTAAAATATCATTACAAT
64 ACATATGAAATTTTAACATAATATAAAATTAACCACATACTAAATTATCAAAATACCATTACAAT
** * * * *
12493 TGGTTTATGAAAATTTGACATGTGATATTTTATTTAAAAATTACTATAATACCACTATTAAATTA
1 TACTTCATAAAAATTTGACATGTGAAATTTTGTTT-AAAATTACTATAATACCACTATTAAATTA
* * * * *
12558 CATATGAAATTTTAACATCATATAAAATTAACTACATACTAAATTATCAAAATACCGTTGTC-GT
65 CATATGAAATTTTAACATAATATAAAATTAACCACATACTAAATTATCAAAATACCATT-ACAAT
* **
12622 TACTTCATAAAAATTTGACATGTGAAATTTTGTTTGAAATTCACTATAATA-GTCTAATTAAATT
1 TACTTCATAAAAATTTGACATGTGAAATTTTGTTTAAAATT-ACTATAATACCACT-ATTAAATT
* * *
12686 ACTTATTAAATGTTAA-ATAATATA
64 ACATATGAAATTTTAACATAATATA
12710 TACTGAAATA
Statistics
Matches: 176, Mismatches: 37, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
128 14 0.08
129 160 0.91
130 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (128 bp):
TACTTCATAAAAATTTGACATGTGAAATTTTGTTTAAAATTACTATAATACCACTATTAAATTAC
ATATGAAATTTTAACATAATATAAAATTAACCACATACTAAATTATCAAAATACCATTACAAT
Found at i:16227 original size:20 final size:21
Alignment explanation
Indices: 16202--16253 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
16192 AGGGCACAAT
16202 AATGGATCTTTAT-TTTGTAA
1 AATGGATCTTTATGTTTGTAA
* *
16222 AATGGAACTTTTATGTTTGTAT
1 AATGGATC-TTTATGTTTGTAA
16244 AATGGATCTT
1 AATGGATCTT
16254 CTTGAATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.26
21 7 0.26
22 13 0.48
ACGTcount: A:0.29, C:0.06, G:0.17, T:0.48
Consensus pattern (21 bp):
AATGGATCTTTATGTTTGTAA
Found at i:24770 original size:11 final size:12
Alignment explanation
Indices: 24739--24773 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
24729 TGATAATAGA
24739 TTTATTTATTTTG
1 TTTATTT-TTTTG
24752 TTTATTTTTTTG
1 TTTATTTTTTTG
24764 TTT-TTTTTTT
1 TTTATTTTTTT
24774 ATGGTAGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 7 0.32
12 8 0.36
13 7 0.32
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.86
Consensus pattern (12 bp):
TTTATTTTTTTG
Done.