Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168238.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_470, 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: 25716
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:1694 original size:13 final size:12
Alignment explanation
Indices: 1676--1705 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1666 AGCTGGGTTT
1676 TGATTGTGATTTG
1 TGATTGTGA-TTG
1689 TGATTGTGATTG
1 TGATTGTGATTG
1701 TGATT
1 TGATT
1706 CTCATTCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (12 bp):
TGATTGTGATTG
Found at i:1695 original size:6 final size:6
Alignment explanation
Indices: 1676--1705 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
1666 AGCTGGGTTT
1676 TGATTG TGATTTG TGATTG TGATTG TGATT
1 TGATTG TGA-TTG TGATTG TGATTG TGATT
1706 CTCATTCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (6 bp):
TGATTG
Found at i:3780 original size:10 final size:10
Alignment explanation
Indices: 3769--3802 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
3759 TATTTTATTT
*
3769 TATAAAAATT
1 TATAAAAATA
3779 TA-AAAAATA
1 TATAAAAATA
3788 TATAAAAATA
1 TATAAAAATA
3798 TATAA
1 TATAA
3803 TTTGATTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TATAAAAATA
Found at i:3850 original size:11 final size:12
Alignment explanation
Indices: 3825--3880 Score: 60
Period size: 13 Copynumber: 4.6 Consensus size: 12
3815 TTTTTTATTT
3825 TTTAATTTAAAA
1 TTTAATTTAAAA
3837 TTTAATTT-AAA
1 TTTAATTTAAAA
*
3848 TTTAATTTATATA
1 TTTAATTTA-AAA
*
3861 TTTAATATTCAAA
1 TTTAAT-TTAAAA
*
3874 CTTAATT
1 TTTAATT
3881 CTAATCAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
11 11 0.30
12 9 0.24
13 15 0.41
14 2 0.05
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTAATTTAAAA
Found at i:4762 original size:2 final size:2
Alignment explanation
Indices: 4757--4808 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
4747 TGTGTGTGTG
4757 TA TA TA TA TA 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 TA TA TA TA TA
4799 TA TA TA TA TA
1 TA TA TA TA TA
4809 AAATTTTAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6467 original size:8 final size:8
Alignment explanation
Indices: 6456--6518 Score: 53
Period size: 8 Copynumber: 8.0 Consensus size: 8
6446 AAATATTAAA
6456 ATTTATAT
1 ATTTATAT
6464 A-TT-TAT
1 ATTTATAT
6470 A-TTATAT
1 ATTTATAT
*
6477 -TTTAATAA
1 ATTT-ATAT
*
6485 AATTATAT
1 ATTTATAT
6493 ATTATATTAT
1 ATT-TA-TAT
6503 ATTTATAT
1 ATTTATAT
6511 ATTTATAT
1 ATTTATAT
6519 TATATTCATA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
6 6 0.13
7 7 0.16
8 20 0.44
9 6 0.13
10 6 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
ATTTATAT
Found at i:6477 original size:11 final size:11
Alignment explanation
Indices: 6461--6529 Score: 59
Period size: 11 Copynumber: 6.0 Consensus size: 11
6451 TTAAAATTTA
6461 TATATTTATAT
1 TATATTTATAT
6472 TATATTT-TAAT
1 TATATTTAT-AT
* *
6483 AAAATTATATAT
1 TATATT-TATAT
*
6495 TATATTATATTT
1 TATATT-TATAT
6507 ATATATTTATAT
1 -TATATTTATAT
*
6519 TATATTCATAT
1 TATATTTATAT
6530 CGTAAATATA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
10 1 0.02
11 23 0.49
12 16 0.34
13 7 0.15
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (11 bp):
TATATTTATAT
Found at i:6495 original size:18 final size:18
Alignment explanation
Indices: 6472--6514 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
6462 ATATTTATAT
6472 TATATTTTAATAAAATTA
1 TATATTTTAATAAAATTA
* * * *
6490 TATATTATATTATATTTA
1 TATATTTTAATAAAATTA
6508 TATATTT
1 TATATTT
6515 ATATTATATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATATTTTAATAAAATTA
Found at i:7872 original size:219 final size:217
Alignment explanation
Indices: 7598--8032 Score: 737
Period size: 219 Copynumber: 2.0 Consensus size: 217
7588 ATTAAAAATA
7598 AATAAAACATGTAAAAATAAAAGTTAGTGATAAAAAAAGGTGAACATAATTTCAAGATAATTAAA
1 AATAAAACATGTAAAAATAAAAGTTAGTGATAAAAAAAGGTGAACATAATTTCAAGATAATTAAA
* *
7663 AAATAATAGGTTAACATTAAACTTAAAGAATATTAATCA-TCTAAAATTTTCCAACTAAATTATT
66 AAAGAATAGGTTAACATTAAACTTAAAGAATATTAATCATTCTAAAAATTTCCAACTAAATTATT
7727 TAATTTATAAAATTGAAAATTTGATAAAAAAATACTACTATAAATGAGAAAAATAGTACTAGTAG
131 TAATTTATAAAATTGAAAATTTGA-AAAAAAATACTACTATAAATGAGAAAAATAGTACTAGTAG
7792 GTGTGAAAAATAAGGGAGGTGTT
195 GTGTGAAAAATAAGGGAGGTGTT
* *
7815 AATATAACATGTAAAAATAAAAGTTAGTGATAAAAAAAAAGGTGAACATAATTTCAAGATAATTC
1 AATAAAACATGTAAAAATAAAAGTTAGTGAT--AAAAAAAGGTGAACATAATTTCAAGATAATTA
* * *
7880 AAAAAGAATAGGTTAACATTAAATTTAAAGAGTATTAATCATTTTAAAAATTTCCAACTAAATTA
64 AAAAAGAATAGGTTAACATTAAACTTAAAGAATATTAATCATTCTAAAAATTTCCAACTAAATTA
* * * *
7945 TTTAATTTATAAAATTGAAATTTTGACAAAAAATAGTACTATAAATGAGAAAAATAGTAGTAGTA
129 TTTAATTTATAAAATTGAAAATTTGAAAAAAAATACTACTATAAATGAGAAAAATAGTACTAGTA
8010 GGTGTGAAAAATAAGGGAGGTGT
194 GGTGTGAAAAATAAGGGAGGTGT
8033 GCAAGGAAGT
Statistics
Matches: 204, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
217 30 0.15
219 128 0.63
220 46 0.23
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (217 bp):
AATAAAACATGTAAAAATAAAAGTTAGTGATAAAAAAAGGTGAACATAATTTCAAGATAATTAAA
AAAGAATAGGTTAACATTAAACTTAAAGAATATTAATCATTCTAAAAATTTCCAACTAAATTATT
TAATTTATAAAATTGAAAATTTGAAAAAAAATACTACTATAAATGAGAAAAATAGTACTAGTAGG
TGTGAAAAATAAGGGAGGTGTT
Found at i:11023 original size:8 final size:8
Alignment explanation
Indices: 11010--11042 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
11000 AGCACTGAAC
11010 AGAGAAAA
1 AGAGAAAA
11018 AGAGAAAA
1 AGAGAAAA
11026 AGAGAAAA
1 AGAGAAAA
11034 AGAGAAAA
1 AGAGAAAA
11042 A
1 A
11043 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAGAAAA
Found at i:11049 original size:16 final size:16
Alignment explanation
Indices: 11014--11050 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
11004 CTGAACAGAG
* *
11014 AAAAAGAGAAAAAGAG
1 AAAAAGAGAAAAAAAA
11030 AAAAAGAGAAAAAAAA
1 AAAAAGAGAAAAAAAA
11046 AAAAA
1 AAAAA
11051 AAAAACACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAGAGAAAAAAAA
Found at i:11660 original size:44 final size:44
Alignment explanation
Indices: 11597--11680 Score: 159
Period size: 44 Copynumber: 1.9 Consensus size: 44
11587 TATTCAACAA
11597 TAATACTTCATTTTTTATTGTCTTTAAGCTGAAAAGCTTCACAG
1 TAATACTTCATTTTTTATTGTCTTTAAGCTGAAAAGCTTCACAG
*
11641 TAATACTTCATTTTTTATTGTGTTTAAGCTGAAAAGCTTC
1 TAATACTTCATTTTTTATTGTCTTTAAGCTGAAAAGCTTC
11681 TTTCTTTGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (44 bp):
TAATACTTCATTTTTTATTGTCTTTAAGCTGAAAAGCTTCACAG
Found at i:16366 original size:18 final size:18
Alignment explanation
Indices: 16332--16372 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
16322 CAATTCGAGT
* * *
16332 TCAAATTCGAGCTCAAAC
1 TCAAATTCGAACACAAAA
16350 TCAAATTCGAACACAAAA
1 TCAAATTCGAACACAAAA
16368 TCAAA
1 TCAAA
16373 CTTTAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.24, G:0.07, T:0.20
Consensus pattern (18 bp):
TCAAATTCGAACACAAAA
Found at i:18133 original size:7 final size:7
Alignment explanation
Indices: 18121--18154 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
18111 CAAATTTAAA
18121 TTAAATT
1 TTAAATT
18128 TTAAATT
1 TTAAATT
18135 TTAAATT
1 TTAAATT
18142 TTAAATT
1 TTAAATT
18149 TTAAAT
1 TTAAAT
18155 CGAGCTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Done.