Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168263.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_493, 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: 24985
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Found at i:1317 original size:26 final size:26
Alignment explanation
Indices: 1267--1317 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1257 TTCATTATTA
* * *
1267 AAGATTACTAAATAATATTTTAAAAC
1 AAGATTACTAAACAATATGTAAAAAC
1293 AAGATTACTAAACAATATGTAAAAA
1 AAGATTACTAAACAATATGTAAAAA
1318 GGTTTTGACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.29
Consensus pattern (26 bp):
AAGATTACTAAACAATATGTAAAAAC
Found at i:3627 original size:62 final size:63
Alignment explanation
Indices: 3543--3739 Score: 208
Period size: 62 Copynumber: 3.1 Consensus size: 63
3533 TTTAGAGTTA
* *
3543 ATATTTTTATAAAAAAATTATTTAAG-GCTTTTTTGTACATAAAACTCTTTAAATAATCTTTTT
1 ATATTTTTATAAATAAATTATTTAAGAACTTTTTTGTACA-AAAACTCTTTAAATAATCTTTTT
* *
3606 ATATTTTT-TTAATAAATTATTTAAGATA-TTTTTTGTACAAAAA-TCCTTAAATTAAT-TATTT
1 ATATTTTTATAAATAAATTATTTAAGA-ACTTTTTTGTACAAAAACTCTTTAAA-TAATCT-TTT
3667 T
63 T
** * * *
3668 ATATTTTTATAAATTGATTATTTAAAGTACTTTTTTTTTACAGAAAACACTTTAAATAATCTTTT
1 ATATTTTTATAAATAAATTATTT-AAGAAC-TTTTTTGTACA-AAAACTCTTTAAATAATCTTTT
3733 T
63 T
3734 -TATTTT
1 ATATTTT
3740 AGGATTTAGG
Statistics
Matches: 112, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
61 8 0.07
62 35 0.31
63 31 0.28
64 3 0.03
65 16 0.14
66 12 0.11
67 7 0.06
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (63 bp):
ATATTTTTATAAATAAATTATTTAAGAACTTTTTTGTACAAAAACTCTTTAAATAATCTTTTT
Found at i:3761 original size:86 final size:84
Alignment explanation
Indices: 3668--3823 Score: 206
Period size: 83 Copynumber: 1.8 Consensus size: 84
3658 TAATTATTTT
** * * * *
3668 ATATTTTTATAAATTGATTATTTAAAGTACTTTTTTTTTACAGAAAACACTTTAAATAA-TCTTT
1 ATATTTTTATAAAAAGATTATTT-AAG-A-TATTTTTATACAAAAAACACCTTAAATAATTCTTT
*
3732 TTTATTTTAGGATTTAGGGTTA
63 TATATTTTAGGATTTAGGGTTA
*
3754 ATATTTTTATAAAAAGATTATTTAAGATATTTTTATACAAAAAATACCTTAAATAATTCTTTTAT
1 ATATTTTTATAAAAAGATTATTTAAGATATTTTTATACAAAAAACACCTTAAATAATTCTTTTAT
3819 ATTTT
66 ATTTT
3824 TATAAATTAA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
83 24 0.39
84 13 0.21
85 3 0.05
86 21 0.34
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (84 bp):
ATATTTTTATAAAAAGATTATTTAAGATATTTTTATACAAAAAACACCTTAAATAATTCTTTTAT
ATTTTAGGATTTAGGGTTA
Found at i:3805 original size:27 final size:26
Alignment explanation
Indices: 3754--3805 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
3744 TTTAGGGTTA
* *
3754 ATATTTTTATAAAAAGATTATTTAAG
1 ATATTTTTATAAAAAGAATACTTAAG
3780 ATATTTTTATACAAAA-AATACCTTAA
1 ATATTTTTATA-AAAAGAATA-CTTAA
3806 ATAATTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (26 bp):
ATATTTTTATAAAAAGAATACTTAAG
Found at i:5371 original size:22 final size:22
Alignment explanation
Indices: 5316--5371 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
5306 ATAAAATATA
*
5316 TTTTATGACAATGGTAATATTTTT
1 TTTTAT-A-AATGGTAAGATTTTT
*
5340 TTTATTTAAATGGTAAGATTTTT
1 TTT-TATAAATGGTAAGATTTTT
5363 TTTTATAAA
1 TTTTATAAA
5372 CAAAAAGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 5 0.18
23 17 0.61
24 4 0.14
25 2 0.07
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (22 bp):
TTTTATAAATGGTAAGATTTTT
Found at i:7754 original size:22 final size:22
Alignment explanation
Indices: 7726--7779 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
7716 TAAGAAAAGG
7726 TTTTTTTTTTTACTTATTTTGC
1 TTTTTTTTTTTACTTATTTTGC
7748 TTTTTTTTTTTACTTATTTTGC
1 TTTTTTTTTTTACTTATTTTGC
7770 TTTTTTTTTT
1 TTTTTTTTTT
7780 CTAAAGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.07, C:0.07, G:0.04, T:0.81
Consensus pattern (22 bp):
TTTTTTTTTTTACTTATTTTGC
Found at i:10686 original size:23 final size:24
Alignment explanation
Indices: 10642--10686 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
10632 AGATCCTTCC
* *
10642 TTTCTTTTTCTGGAGATTGCACTT
1 TTTCTTTTTCTAGAGATAGCACTT
10666 TTTCTTTTTCTAGAGA-AGCAC
1 TTTCTTTTTCTAGAGATAGCAC
10687 GGTTGAAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (24 bp):
TTTCTTTTTCTAGAGATAGCACTT
Found at i:10868 original size:3 final size:3
Alignment explanation
Indices: 10860--10887 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
10850 AATGATCGTG
10860 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
10888 AGGTTTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:12676 original size:13 final size:13
Alignment explanation
Indices: 12658--12682 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12648 GAATTTTTTT
12658 TCAAATATAATTA
1 TCAAATATAATTA
12671 TCAAATATAATT
1 TCAAATATAATT
12683 CAATATTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
TCAAATATAATTA
Found at i:17452 original size:38 final size:40
Alignment explanation
Indices: 17409--17488 Score: 119
Period size: 38 Copynumber: 2.0 Consensus size: 40
17399 CCTGTCAGTC
* *
17409 AACAAAATGGAAAATTTA-CCA-AATGCTTAGTGGGATTG
1 AACAAAATGGAAAATTAACCCAGAATGCTTAGTGGGACTG
*
17447 AACAAAATGGAAAATTAACCCAGAATTCTTAGTGGGACTG
1 AACAAAATGGAAAATTAACCCAGAATGCTTAGTGGGACTG
17487 AA
1 AA
17489 AGGATTGGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 17 0.46
39 3 0.08
40 17 0.46
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (40 bp):
AACAAAATGGAAAATTAACCCAGAATGCTTAGTGGGACTG
Done.