Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168031.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_284, 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: 38925
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:2848 original size:2 final size:2
Alignment explanation
Indices: 2841--2872 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2831 ACTGATAATT
2841 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2873 CACGTATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10354 original size:16 final size:16
Alignment explanation
Indices: 10329--10366 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
10319 TTTGTGAATA
10329 TTTT-TTTACTTAATT
1 TTTTATTTACTTAATT
*
10344 TTTTATTTACTTGATT
1 TTTTATTTACTTAATT
*
10360 TTATATT
1 TTTTATT
10367 CTAAAATCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTATTTACTTAATT
Found at i:17719 original size:19 final size:19
Alignment explanation
Indices: 17670--17719 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
17660 AATATGATAC
* *
17670 GATACGATTAACACGATTA
1 GATACGATTAATACAATTA
* * *
17689 TATATGAATAATACAATTA
1 GATACGATTAATACAATTA
17708 GATACGATTAAT
1 GATACGATTAAT
17720 TCATTTATTT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (19 bp):
GATACGATTAATACAATTA
Found at i:17778 original size:17 final size:18
Alignment explanation
Indices: 17756--17790 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17746 TAAATTAGCA
17756 TTTAAA-TAAATAATTAT
1 TTTAAATTAAATAATTAT
*
17773 TTTAAATTAAATATTTAT
1 TTTAAATTAAATAATTAT
17791 AATATATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAAATTAAATAATTAT
Found at i:19520 original size:18 final size:18
Alignment explanation
Indices: 19470--19521 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 18
19460 AGAATATTTG
*
19470 TTAAAAA-AAATTAAAAA
1 TTAAAAACAAAATAAAAA
*
19487 -TATAAACAAATTATAAAAA
1 TTAAAAACAAA--ATAAAAA
19506 TTAAAAACAAAATAAA
1 TTAAAAACAAAATAAA
19522 TTATTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
16 5 0.18
17 3 0.11
18 5 0.18
19 6 0.21
20 9 0.32
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (18 bp):
TTAAAAACAAAATAAAAA
Found at i:19522 original size:25 final size:26
Alignment explanation
Indices: 19475--19525 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
19465 ATTTGTTAAA
*
19475 AAAAATTAAAAATATAAACAAATTAT
1 AAAAATTAAAAACATAAACAAATTAT
*
19501 AAAAATTAAAAACA-AAATAAATTAT
1 AAAAATTAAAAACATAAACAAATTAT
19526 TTTTATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (26 bp):
AAAAATTAAAAACATAAACAAATTAT
Found at i:19724 original size:22 final size:22
Alignment explanation
Indices: 19696--19753 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
19686 TTAAAATTAA
19696 AATATTTTAAAATTTTTAATTT
1 AATATTTTAAAATTTTTAATTT
* *
19718 AATATTTTAAAAAGTTCTAATTT
1 AATATTTT-AAAATTTTTAATTT
19741 --T-TTTTAAAATTTT
1 AATATTTTAAAATTTT
19754 GAAATATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 6 0.19
20 4 0.13
21 1 0.03
22 8 0.26
23 12 0.39
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
AATATTTTAAAATTTTTAATTT
Found at i:19818 original size:25 final size:23
Alignment explanation
Indices: 19740--19817 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 23
19730 AGTTCTAATT
** *
19740 TTTTTTAAAATTTTGAAA-TATTA
1 TTTTTTAAAAAATT-AAATTATGA
*
19763 TTTTTTAAAAAATTAAATTTTGA
1 TTTTTTAAAAAATTAAATTATGA
19786 TTTTTTTAAAAAACTTAAAATATATGA
1 -TTTTTTAAAAAA-TT-AAAT-TATGA
19813 TTTTT
1 TTTTT
19818 ATTAGTAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
22 3 0.07
23 15 0.33
24 12 0.27
25 2 0.04
26 9 0.20
27 4 0.09
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (23 bp):
TTTTTTAAAAAATTAAATTATGA
Found at i:21604 original size:30 final size:31
Alignment explanation
Indices: 21551--21610 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
21541 TATATATATT
*
21551 ATTTAAATACTTTTATAAAAAAAATCAAATG
1 ATTTAAATACTTTTATAAAAAAAATAAAATG
*
21582 ATTTAAGTACTTTTAT-AAAAAAATAAAAT
1 ATTTAAATACTTTTATAAAAAAAATAAAAT
21611 TAGCCGTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (31 bp):
ATTTAAATACTTTTATAAAAAAAATAAAATG
Found at i:21958 original size:15 final size:16
Alignment explanation
Indices: 21940--21977 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
21930 ATATAAAAAT
21940 AATAAATAAAA-TAAA
1 AATAAATAAAATTAAA
*
21955 AAT-ATTAAAATTAAA
1 AATAAATAAAATTAAA
21970 AATAAATA
1 AATAAATA
21978 TAGTATTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 6 0.32
15 10 0.53
16 3 0.16
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAATAAAATTAAA
Found at i:22040 original size:26 final size:27
Alignment explanation
Indices: 22010--22072 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 27
22000 TTTTTTTTAT
22010 TTTTATATTATATTATGATTATTGT--
1 TTTTATATTATATTATGATTATTGTAC
*
22035 GTTT-TATTA-ATTATGATTATTGTAC
1 TTTTATATTATATTATGATTATTGTAC
22060 TTTTCATATTATA
1 TTTT-ATATTATA
22073 AATTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
23 14 0.45
24 5 0.16
25 6 0.19
27 5 0.16
28 1 0.03
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.60
Consensus pattern (27 bp):
TTTTATATTATATTATGATTATTGTAC
Found at i:23053 original size:6 final size:6
Alignment explanation
Indices: 23032--23113 Score: 67
Period size: 6 Copynumber: 12.7 Consensus size: 6
23022 ATAAACAAGC
* *
23032 AAATCAA AACATAA AAATAAA AAATAA ATATAA CAAAAATA AAATAA AAA-AGA
1 AAAT-AA AA-ATAA AAAT-AA AAATAA AAATAA -AAATA-A AAATAA AAATA-A
*
23085 AAAAACA AAATAA AAATAA AAATAA AAAT
1 AAATA-A AAATAA AAATAA AAATAA AAAT
23114 TGATTTGCTT
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
5 1 0.02
6 34 0.54
7 25 0.40
8 3 0.05
ACGTcount: A:0.79, C:0.05, G:0.01, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:23071 original size:11 final size:10
Alignment explanation
Indices: 23044--23111 Score: 57
Period size: 11 Copynumber: 6.5 Consensus size: 10
23034 ATCAAAACAT
23044 AAAAATAAAA
1 AAAAATAAAA
*
23054 AATAAATATAAC
1 AA-AAATA-AAA
23066 AAAAATAAAA
1 AAAAATAAAA
* *
23076 TAAAA-AAGA
1 AAAAATAAAA
*
23085 AAAAACAAAA
1 AAAAATAAAA
23095 TAAAAATAAAA
1 -AAAAATAAAA
23106 ATAAAA
1 A-AAAA
23112 ATTGATTTGC
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
9 7 0.15
10 12 0.26
11 23 0.50
12 4 0.09
ACGTcount: A:0.82, C:0.03, G:0.01, T:0.13
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:23080 original size:25 final size:26
Alignment explanation
Indices: 23042--23112 Score: 83
Period size: 25 Copynumber: 2.7 Consensus size: 26
23032 AAATCAAAAC
* *
23042 ATAAAAATAAAAAATAAATATAACAAA
1 ATAAAAAT-AAAAATAAAAAAAACAAA
*
23069 A-ATAAAATAAAAA-AGAAAAAACAAA
1 ATA-AAAATAAAAATAAAAAAAACAAA
23094 ATAAAAATAAAAATAAAAA
1 ATAAAAATAAAAATAAAAA
23113 TTGATTTGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
25 20 0.54
26 11 0.30
27 6 0.16
ACGTcount: A:0.82, C:0.03, G:0.01, T:0.14
Consensus pattern (26 bp):
ATAAAAATAAAAATAAAAAAAACAAA
Found at i:23107 original size:12 final size:12
Alignment explanation
Indices: 23032--23113 Score: 67
Period size: 13 Copynumber: 6.3 Consensus size: 12
23022 ATAAACAAGC
23032 AAATCAAAACATAA
1 AAAT-AAAA-ATAA
23046 AAATAAAAAATAA
1 AAAT-AAAAATAA
* *
23059 ATATAACAAAAATA
1 AAATAA-AAATA-A
23073 AAATAAAAA-AGA
1 AAATAAAAATA-A
*
23085 AAAAACAAAATAA
1 AAATA-AAAATAA
23098 AAATAAAAATAA
1 AAATAAAAATAA
23110 AAAT
1 AAAT
23114 TGATTTGCTT
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
12 19 0.33
13 23 0.40
14 15 0.26
ACGTcount: A:0.79, C:0.05, G:0.01, T:0.15
Consensus pattern (12 bp):
AAATAAAAATAA
Found at i:29976 original size:16 final size:17
Alignment explanation
Indices: 29943--29978 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
29933 GAAATAAAAA
*
29943 TAAAAATTGATATGATT
1 TAAAAATTGATATAATT
29960 TAAAAATTGATA-AATT
1 TAAAAATTGATATAATT
29976 TAA
1 TAA
29979 TAAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (17 bp):
TAAAAATTGATATAATT
Done.