Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168002.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_258, 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: 41764
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:9878 original size:17 final size:17
Alignment explanation
Indices: 9858--9891 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9848 ATCATATAGG
*
9858 ATATTAAATTAAAAATT
1 ATATTAAATAAAAAATT
*
9875 ATATTTAATAAAAAATT
1 ATATTAAATAAAAAATT
9892 TTAAAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATTAAATAAAAAATT
Found at i:9913 original size:9 final size:9
Alignment explanation
Indices: 9886--9937 Score: 56
Period size: 8 Copynumber: 6.0 Consensus size: 9
9876 TATTTAATAA
9886 AAAATTT-T
1 AAAATTTAT
9894 AAAATTT-T
1 AAAATTTAT
9902 AAAATTTAT
1 AAAATTTAT
*
9911 AAAATTAAT
1 AAAATTTAT
*
9920 AAATAATTAT
1 AAA-ATTTAT
9930 -AAATTTAT
1 AAAATTTAT
9938 TCAAATAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
8 20 0.53
9 14 0.37
10 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAATTTAT
Found at i:9943 original size:20 final size:19
Alignment explanation
Indices: 9879--9947 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
9869 AAAATTATAT
* *
9879 TTAATAAAAAATTTTAAAA
1 TTAATAAATAATTATAAAA
* *
9898 TT-TTAAA-ATTTATAAAA
1 TTAATAAATAATTATAAAA
*
9915 TTAATAAATAATTATAAAT
1 TTAATAAATAATTATAAAA
*
9934 TTATTCAAATAATT
1 TTAAT-AAATAATT
9948 TATGTCAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
17 10 0.25
18 8 0.20
19 14 0.35
20 8 0.20
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAATAAATAATTATAAAA
Found at i:9949 original size:13 final size:14
Alignment explanation
Indices: 9931--9960 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
9921 AATAATTATA
9931 AATTTAT-TCAAAT
1 AATTTATGTCAAAT
9944 AATTTATGTCAAAT
1 AATTTATGTCAAAT
9958 AAT
1 AAT
9961 AATTTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (14 bp):
AATTTATGTCAAAT
Found at i:9996 original size:52 final size:53
Alignment explanation
Indices: 9914--10033 Score: 129
Period size: 52 Copynumber: 2.2 Consensus size: 53
9904 AATTTATAAA
* ** *
9914 ATTAATAAATAATTATAAATTTATTCAAATAAT-TTATGTCAAATAATA-ATTT
1 ATTAATAAATAATTATAAATTAATAAAAATAATATT-TATCAAATAATATATTT
*
9966 ATTAATAAATAATTGAT-AATTAATAAAAATAATAATTTATCAAATAATATTTTT
1 ATTAATAAATAATT-ATAAATTAATAAAAATAAT-ATTTATCAAATAATATATTT
10020 ATTATATTAAATAA
1 ATTA-A-TAAATAA
10034 AAAATTAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
52 27 0.47
53 13 0.23
54 9 0.16
55 1 0.02
56 7 0.12
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.43
Consensus pattern (53 bp):
ATTAATAAATAATTATAAATTAATAAAAATAATATTTATCAAATAATATATTT
Found at i:11793 original size:16 final size:16
Alignment explanation
Indices: 11772--11804 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
11762 ATAGTATATC
11772 TCCATAAAGTCCATAA
1 TCCATAAAGTCCATAA
*
11788 TCCATAAAGTCCTTAA
1 TCCATAAAGTCCATAA
11804 T
1 T
11805 TGAAGCCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.30
Consensus pattern (16 bp):
TCCATAAAGTCCATAA
Found at i:15221 original size:12 final size:12
Alignment explanation
Indices: 15204--15232 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
15194 TTTGTTAGAA
15204 ATTTTATTAATT
1 ATTTTATTAATT
15216 ATTTTATTAATT
1 ATTTTATTAATT
15228 -TTTTA
1 ATTTTA
15233 ATTTTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
ATTTTATTAATT
Found at i:15896 original size:14 final size:14
Alignment explanation
Indices: 15877--15927 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
15867 AGTACCCGTT
*
15877 CGGTTCGGTCTAAG
1 CGGTTCGATCTAAG
* *
15891 CGGTTCGATTTCAG
1 CGGTTCGATCTAAG
15905 TTCGGTTCGATCTAAG
1 --CGGTTCGATCTAAG
15921 CGGTTCG
1 CGGTTCG
15928 GTTCCAATCC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 18 0.60
16 12 0.40
ACGTcount: A:0.14, C:0.22, G:0.31, T:0.33
Consensus pattern (14 bp):
CGGTTCGATCTAAG
Found at i:15896 original size:30 final size:30
Alignment explanation
Indices: 15860--15927 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
15850 GTTCGATCCG
* *
15860 GCGGTTC-AGTACCCGTTCGGTTCGGTCTAA
1 GCGGTTCGA-TACCAGTTCGGTTCGATCTAA
**
15890 GCGGTTCGATTTCAGTTCGGTTCGATCTAA
1 GCGGTTCGATACCAGTTCGGTTCGATCTAA
15920 GCGGTTCG
1 GCGGTTCG
15928 GTTCCAATCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.32
Consensus pattern (30 bp):
GCGGTTCGATACCAGTTCGGTTCGATCTAA
Found at i:16834 original size:9 final size:9
Alignment explanation
Indices: 16817--16865 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 9
16807 CAGAGACGGG
16817 AAGAAAAGA
1 AAGAAAAGA
*
16826 AAGAGAAG-
1 AAGAAAAGA
16834 AAG-AAA-A
1 AAGAAAAGA
*
16841 AGGAAAAGA
1 AAGAAAAGA
16850 AAGAAAAGA
1 AAGAAAAGA
16859 AAGAAAA
1 AAGAAAA
16866 AAAATTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
7 4 0.12
8 6 0.18
9 23 0.70
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAGAAAAGA
Found at i:16847 original size:24 final size:25
Alignment explanation
Indices: 16819--16866 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
16809 GAGACGGGAA
*
16819 GAAAAGAAAGAGAAG-AAGAAAAAG
1 GAAAAGAAAGAAAAGAAAGAAAAAG
16843 GAAAAGAAAGAAAAGAAAGAAAAA
1 GAAAAGAAAGAAAAGAAAGAAAAA
16867 AAATTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (25 bp):
GAAAAGAAAGAAAAGAAAGAAAAAG
Found at i:16879 original size:3 final size:3
Alignment explanation
Indices: 16873--16920 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
16863 AAAAAAATTA
16873 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16921 CAAAATGGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:21480 original size:17 final size:17
Alignment explanation
Indices: 21424--21498 Score: 57
Period size: 17 Copynumber: 4.4 Consensus size: 17
21414 TATCCAATTA
*
21424 AAAATAAAT-AGAAAAAC
1 AAAA-AAATGAGAAAAAT
* *
21441 AAAAAAGATTAAAAAAAGT
1 AAAAAA-ATGAGAAAAA-T
*
21460 -AAAATATGAG-AAAAT
1 AAAAAAATGAGAAAAAT
*
21475 AAAAAAATGGGAAAAAT
1 AAAAAAATGAGAAAAAT
21492 AAAAAAA
1 AAAAAAA
21499 GCTCATAGCT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
15 1 0.02
16 14 0.30
17 21 0.46
18 10 0.22
ACGTcount: A:0.75, C:0.01, G:0.11, T:0.13
Consensus pattern (17 bp):
AAAAAAATGAGAAAAAT
Found at i:28754 original size:28 final size:28
Alignment explanation
Indices: 28714--28767 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
28704 TGTCCTTAAC
28714 ATGGAACAAGTGACAATAGCAAGGGGAA
1 ATGGAACAAGTGACAATAGCAAGGGGAA
*
28742 ATGGAACAAGTGACAGTAGCAAGGGG
1 ATGGAACAAGTGACAATAGCAAGGGG
28768 CGATAATACG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.11, G:0.35, T:0.11
Consensus pattern (28 bp):
ATGGAACAAGTGACAATAGCAAGGGGAA
Found at i:29411 original size:10 final size:10
Alignment explanation
Indices: 29387--29416 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
29377 TATTTTATCA
29387 ATTAAAATA-
1 ATTAAAATAT
29396 ATTAAAATAT
1 ATTAAAATAT
29406 ATTAAAATAT
1 ATTAAAATAT
29416 A
1 A
29417 AAAATTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:29428 original size:19 final size:19
Alignment explanation
Indices: 29383--29430 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
29373 AAAATATTTT
*
29383 ATCAATTAAAATAATTAAA
1 ATCAATTAAAATAATAAAA
29402 AT-ATATTAAAAT-ATAAAA
1 ATCA-ATTAAAATAATAAAA
29420 ATTCAATTAAA
1 A-TCAATTAAA
29431 CTTGTGAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 7 0.28
19 17 0.68
20 1 0.04
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
ATCAATTAAAATAATAAAA
Found at i:33656 original size:35 final size:35
Alignment explanation
Indices: 33607--33674 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
33597 TGAAATATTA
* *
33607 ATAAATTTTAATTTGAAAAAATAAATTATAAAATT
1 ATAAACTTTAATTTGAAAAAATAAAGTATAAAATT
* *
33642 ATAAACTTTGATTTGAAAAGATAAAGTATAAAA
1 ATAAACTTTAATTTGAAAAAATAAAGTATAAAA
33675 AAAATTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.35
Consensus pattern (35 bp):
ATAAACTTTAATTTGAAAAAATAAAGTATAAAATT
Found at i:34408 original size:15 final size:16
Alignment explanation
Indices: 34384--34421 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
34374 TGAATATTAG
34384 TTTA-AATATAAAA-A
1 TTTATAATATAAAATA
34398 TTTATAATATAAAATA
1 TTTATAATATAAAATA
*
34414 ATTATAAT
1 TTTATAAT
34422 TTTAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 9 0.43
16 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTATAATATAAAATA
Done.