Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168417.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_631, 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: 21047
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Found at i:2036 original size:21 final size:21
Alignment explanation
Indices: 2006--2047 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1996 TCCTTATCAC
*
2006 TTTGAATATCAACATTACCAA
1 TTTGAATATCAACATCACCAA
* *
2027 TTTGAGTATCAGCATCACCAA
1 TTTGAATATCAACATCACCAA
2048 CTTAAGGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (21 bp):
TTTGAATATCAACATCACCAA
Found at i:6567 original size:2 final size:2
Alignment explanation
Indices: 6560--6605 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
6550 TACTTTCTGG
* *
6560 AT AT AT AT AT AT AT AT AT AT GT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6602 AT AT
1 AT AT
6606 GCTGGTCTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8808 original size:6 final size:6
Alignment explanation
Indices: 8797--8867 Score: 71
Period size: 6 Copynumber: 12.3 Consensus size: 6
8787 AACAAAAATT
* *
8797 AATAAA AATAAA AA-ATAA AA-AAA ACTCAA AAT--A AATAGAA AAT-AA
1 AATAAA AATAAA AATA-AA AATAAA AATAAA AATAAA AATA-AA AATAAA
8842 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
8868 CCTACGATAC
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
4 4 0.07
5 9 0.16
6 39 0.70
7 4 0.07
ACGTcount: A:0.80, C:0.03, G:0.01, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:8809 original size:16 final size:16
Alignment explanation
Indices: 8790--8865 Score: 82
Period size: 17 Copynumber: 4.6 Consensus size: 16
8780 AAAAACCAAC
*
8790 AAAAATTAATAAAAAT
1 AAAAATAAATAAAAAT
8806 AAAAAATAAA-AAAAACT
1 -AAAAATAAATAAAAA-T
*
8823 CAAAATAAATAGAAAAT
1 AAAAATAAATA-AAAAT
*
8840 AAAATAAAAATAAAAAT
1 AAAA-ATAAATAAAAAT
8857 AAAAATAAA
1 AAAAATAAA
8866 AACCTACGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
16 17 0.34
17 23 0.46
18 10 0.20
ACGTcount: A:0.79, C:0.03, G:0.01, T:0.17
Consensus pattern (16 bp):
AAAAATAAATAAAAAT
Found at i:8815 original size:33 final size:34
Alignment explanation
Indices: 8776--8865 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
8766 TTCTGAAATT
* *
8776 AAATAAAAACCAAC-AAAAATTAATA-AAAATAAA
1 AAATAAAAA-AAACTAAAAATAAATAGAAAATAAA
*
8809 AAATAAAAAAAACTCAAAATAAATAGAAAATAAA
1 AAATAAAAAAAACTAAAAATAAATAGAAAATAAA
8843 ATAA-AAATAAAAA-TAAAAATAAA
1 A-AATAAA-AAAAACTAAAAATAAA
8866 AACCTACGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
32 3 0.06
33 18 0.37
34 21 0.43
35 7 0.14
ACGTcount: A:0.78, C:0.06, G:0.01, T:0.16
Consensus pattern (34 bp):
AAATAAAAAAAACTAAAAATAAATAGAAAATAAA
Found at i:8820 original size:11 final size:11
Alignment explanation
Indices: 8800--8867 Score: 57
Period size: 11 Copynumber: 6.0 Consensus size: 11
8790 AAAAATTAAT
8800 AAAAATAAAAA
1 AAAAATAAAAA
*
8811 ATAAAA-AAAACT
1 A-AAAATAAAA-A
* *
8823 CAAAATAAATA
1 AAAAATAAAAA
* *
8834 GAAAATAAAAT
1 AAAAATAAAAA
8845 AAAAATAAAAA
1 AAAAATAAAAA
8856 TAAAAATAAAAA
1 -AAAAATAAAAA
8868 CCTACGATAC
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
11 26 0.59
12 18 0.41
ACGTcount: A:0.81, C:0.03, G:0.01, T:0.15
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:9734 original size:18 final size:20
Alignment explanation
Indices: 9668--9735 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 20
9658 ATAACGACAC
*
9668 TAATAATAATAATAATAATAA
1 TAATAAT-ATAATAATAGTAA
9689 TAATAATAATAATAATAGTAA
1 TAATAAT-ATAATAATAGTAA
* *
9710 TAGTAATATAAT-ATGGT-A
1 TAATAATATAATAATAGTAA
9728 TAATAATA
1 TAATAATA
9736 ACGATAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
18 8 0.19
19 4 0.09
20 5 0.12
21 26 0.60
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (20 bp):
TAATAATATAATAATAGTAA
Found at i:9736 original size:3 final size:3
Alignment explanation
Indices: 9668--9722 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
9658 ATAACGACAC
* *
9668 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9716 T-A TAA TA
1 TAA TAA TA
9723 TGGTATAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:9872 original size:21 final size:21
Alignment explanation
Indices: 9848--9887 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9838 CTAATAGTAT
9848 TAGTAT-AGTATTATACTACCA
1 TAGTATCA-TATTATACTACCA
*
9869 TAGTATCATATTGTACTAC
1 TAGTATCATATTATACTAC
9888 TACAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (21 bp):
TAGTATCATATTATACTACCA
Found at i:16729 original size:53 final size:52
Alignment explanation
Indices: 16632--16740 Score: 139
Period size: 53 Copynumber: 2.1 Consensus size: 52
16622 ATCTCTTATG
* * * *
16632 ATAAGTGTATGAGGTTACTAGTTTATCAATTCAACCTCGTATAAAGCA-TCAT
1 ATAAGTGCATAAGGCTACTAGTTTATCAATTCAACCTCATATAAAG-AGTCAT
* *
16684 ATAAGTGCATAAGGCTACTAGTTGTATTAGTTCAACCTCATATAAAGAGTCAT
1 ATAAGTGCATAAGGCTACTAGTT-TATCAATTCAACCTCATATAAAGAGTCAT
16737 ATAA
1 ATAA
16741 CTGCCCAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
52 21 0.43
53 28 0.57
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (52 bp):
ATAAGTGCATAAGGCTACTAGTTTATCAATTCAACCTCATATAAAGAGTCAT
Done.