Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168423.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_637, 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: 20944
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:2459 original size:5 final size:5
Alignment explanation
Indices: 2449--2500 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
2439 ACAATGAGTG
*
2449 AAAAT AAAAT AAAAT AGAAAT AAAA- AAAAT AAAAAT AAAAT GAAAAA
1 AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT -AAAAT AAAAT -AAAAT
2496 AAAAT
1 AAAAT
2501 CTACGATCGG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 4 0.10
5 23 0.56
6 14 0.34
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:2477 original size:25 final size:24
Alignment explanation
Indices: 2449--2499 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 24
2439 ACAATGAGTG
2449 AAAAT-AAAATAAAATAGAAATAAAA
1 AAAATAAAAATAAAAT-GAAA-AAAA
2474 AAAATAAAAATAAAATGAAAAAAA
1 AAAATAAAAATAAAATGAAAAAAA
2498 AA
1 AA
2500 TCTACGATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 6 0.24
25 9 0.36
26 10 0.40
ACGTcount: A:0.82, C:0.00, G:0.04, T:0.14
Consensus pattern (24 bp):
AAAATAAAAATAAAATGAAAAAAA
Found at i:2479 original size:15 final size:16
Alignment explanation
Indices: 2449--2500 Score: 72
Period size: 15 Copynumber: 3.3 Consensus size: 16
2439 ACAATGAGTG
2449 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
*
2465 GAAATAAAA-AAAATA
1 AAAATAAAATAAAATA
2480 AAAATAAAATGAAAA-A
1 AAAATAAAAT-AAAATA
2496 AAAAT
1 AAAAT
2501 CTACGATCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 14 0.44
16 14 0.44
17 4 0.12
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:2483 original size:21 final size:20
Alignment explanation
Indices: 2447--2498 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
2437 AAACAATGAG
2447 TGAAAATAAAATAAAATAGAAA
1 TGAAAA-AAAATAAAATA-AAA
2469 T-AAAAAAAATAAAAATAAAA
1 TGAAAAAAAAT-AAAATAAAA
2489 TGAAAAAAAA
1 TGAAAAAAAA
2499 ATCTACGATC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.32
21 18 0.64
22 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (20 bp):
TGAAAAAAAATAAAATAAAA
Found at i:5186 original size:12 final size:12
Alignment explanation
Indices: 5169--5195 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5159 CATGGTCACG
5169 CTTTTTGCCGTT
1 CTTTTTGCCGTT
5181 CTTTTTGCCGTT
1 CTTTTTGCCGTT
5193 CTT
1 CTT
5196 CTTAAAGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.26, G:0.15, T:0.59
Consensus pattern (12 bp):
CTTTTTGCCGTT
Found at i:5574 original size:46 final size:46
Alignment explanation
Indices: 5492--5583 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
5482 ACATGTGAAT
* * ** *
5492 TAATTGCATAAATCAAGCACCGAATTTTTTTACAAAATCTTTAACG
1 TAATTGCATAAATCAAGCACCAAAATTTACTACAAAATCTTCAACG
* *
5538 TAATTGCATGAATCAAGCACCAAAATTTACTGCAAAATCTTCAACG
1 TAATTGCATAAATCAAGCACCAAAATTTACTACAAAATCTTCAACG
5584 ATTTTTTCTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (46 bp):
TAATTGCATAAATCAAGCACCAAAATTTACTACAAAATCTTCAACG
Found at i:19639 original size:19 final size:18
Alignment explanation
Indices: 19609--19644 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
19599 TGAATCCAAA
19609 AAATTTTTAAATCTAAAT
1 AAATTTTTAAATCTAAAT
*
19627 AAATTTATTAAATTTAAA
1 AAATTT-TTAAATCTAAA
19645 AAAAAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTTTTAAATCTAAAT
Found at i:20020 original size:127 final size:127
Alignment explanation
Indices: 19839--20095 Score: 514
Period size: 127 Copynumber: 2.0 Consensus size: 127
19829 AACCTGTATG
19839 CAAGATTTATATAACTGACGGTGGCTATGATTTGCCTCTTTGTGATCATTCGTCTCTAGAAAAAT
1 CAAGATTTATATAACTGACGGTGGCTATGATTTGCCTCTTTGTGATCATTCGTCTCTAGAAAAAT
19904 CTAATTCTCACGTCCACAAAAAGTGATACTTGTCTTAATTCCTATTCAAAATGTAAACATGA
66 CTAATTCTCACGTCCACAAAAAGTGATACTTGTCTTAATTCCTATTCAAAATGTAAACATGA
19966 CAAGATTTATATAACTGACGGTGGCTATGATTTGCCTCTTTGTGATCATTCGTCTCTAGAAAAAT
1 CAAGATTTATATAACTGACGGTGGCTATGATTTGCCTCTTTGTGATCATTCGTCTCTAGAAAAAT
20031 CTAATTCTCACGTCCACAAAAAGTGATACTTGTCTTAATTCCTATTCAAAATGTAAACATGA
66 CTAATTCTCACGTCCACAAAAAGTGATACTTGTCTTAATTCCTATTCAAAATGTAAACATGA
20093 CAA
1 CAA
20096 TGACGCATCC
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 130 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (127 bp):
CAAGATTTATATAACTGACGGTGGCTATGATTTGCCTCTTTGTGATCATTCGTCTCTAGAAAAAT
CTAATTCTCACGTCCACAAAAAGTGATACTTGTCTTAATTCCTATTCAAAATGTAAACATGA
Found at i:20372 original size:7 final size:7
Alignment explanation
Indices: 20350--20389 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
20340 TTTGTTATCA
20350 AAATTTT
1 AAATTTT
*
20357 -AATTCT
1 AAATTTT
20363 AAATTTT
1 AAATTTT
20370 AAATTTT
1 AAATTTT
20377 -AATTTT
1 AAATTTT
20383 AAATTTT
1 AAATTTT
20390 TATAAATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 11 0.38
7 18 0.62
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (7 bp):
AAATTTT
Found at i:20373 original size:20 final size:20
Alignment explanation
Indices: 20350--20389 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
20340 TTTGTTATCA
20350 AAATTTTAATTCTAAATTTT
1 AAATTTTAATTCTAAATTTT
*
20370 AAATTTTAATTTTAAATTTT
1 AAATTTTAATTCTAAATTTT
20390 TATAAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
AAATTTTAATTCTAAATTTT
Found at i:20385 original size:13 final size:13
Alignment explanation
Indices: 20351--20389 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
20341 TTGTTATCAA
*
20351 AATTTT-AATTCTA
1 AATTTTAAATT-TT
20364 AATTTTAAATTTT
1 AATTTTAAATTTT
20377 AATTTTAAATTTT
1 AATTTTAAATTTT
20390 TATAAATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 20 0.83
14 4 0.17
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (13 bp):
AATTTTAAATTTT
Found at i:20864 original size:25 final size:25
Alignment explanation
Indices: 20835--20926 Score: 89
Period size: 25 Copynumber: 3.6 Consensus size: 25
20825 AATTTAAAAT
20835 TTAAATAAATAACAAATAAAAAT-AA
1 TTAAATAAA-AACAAATAAAAATAAA
**
20860 TTAAATAAAATTAAATAAAAATAAA
1 TTAAATAAAAACAAATAAAAATAAA
*
20885 ATAAAT-AAAACAAACTAATAAAGTAAA
1 TTAAATAAAAACAAA-TAA-AAA-TAAA
* *
20912 ATAATTAAAAACAAA
1 TTAAATAAAAACAAA
20927 AATTATGTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
24 17 0.30
25 19 0.34
26 3 0.05
27 9 0.16
28 8 0.14
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.23
Consensus pattern (25 bp):
TTAAATAAAAACAAATAAAAATAAA
Found at i:20867 original size:14 final size:14
Alignment explanation
Indices: 20848--20893 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
20838 AATAAATAAC
*
20848 AAATAAAAATAATT
1 AAATAAAAATAAAT
*
20862 AAATAAAATTAAAT
1 AAATAAAAATAAAT
*
20876 AAAAATAAAATAAAT
1 AAATA-AAAATAAAT
20891 AAA
1 AAA
20894 ACAAACTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAAAAATAAAT
Done.