Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168375.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_594, 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: 21985
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Found at i:1199 original size:29 final size:29
Alignment explanation
Indices: 1136--1199 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
1126 AAATTCCTTA
* *
1136 AAAAATAATACTATAAGGATTAAATTTTT
1 AAAAATAATACTATAAGGACTAAATTATT
** *
1165 TTAAATAATATTAT-AGGAACTAAATTATT
1 AAAAATAATACTATAAGG-ACTAAATTATT
1194 AAAAAT
1 AAAAAT
1200 CGAATAGTAC
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
28 3 0.11
29 24 0.89
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (29 bp):
AAAAATAATACTATAAGGACTAAATTATT
Found at i:6560 original size:15 final size:15
Alignment explanation
Indices: 6542--6584 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
6532 AAAATATTAA
6542 AAATTATTTATTATT
1 AAATTATTTATTATT
6557 AAA-TA--TATTA--
1 AAATTATTTATTATT
6567 AAATTATTTATTATT
1 AAATTATTTATTATT
6582 AAA
1 AAA
6585 ACTATTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 10
0.70 0.00 0.30
Matches are distributed among these distances:
10 3 0.13
11 2 0.09
12 5 0.22
13 5 0.22
14 2 0.09
15 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AAATTATTTATTATT
Found at i:6569 original size:25 final size:24
Alignment explanation
Indices: 6527--6592 Score: 105
Period size: 25 Copynumber: 2.6 Consensus size: 24
6517 ATTGATATAT
6527 TTATTAAAATATTAAAAATTATTTA
1 TTATTAAAATATT-AAAATTATTTA
6552 TTATTAAATATATTAAAATTATTTA
1 TTATTAAA-ATATTAAAATTATTTA
6577 TTATTAAAACTATTAA
1 TTATTAAAA-TATTAA
6593 TAATAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
24 1 0.03
25 33 0.85
26 5 0.13
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TTATTAAAATATTAAAATTATTTA
Found at i:6581 original size:16 final size:16
Alignment explanation
Indices: 6551--6605 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
6541 AAAATTATTT
6551 ATTATTAAATATATTAAA
1 ATTATT-AAT-TATTAAA
*
6569 ATTATTTATTATTAAA
1 ATTATTAATTATTAAA
* * *
6585 ACTATTAATAATAAAA
1 ATTATTAATTATTAAA
6601 ATTAT
1 ATTAT
6606 ATTTTAATTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
16 23 0.74
17 2 0.06
18 6 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTATTAATTATTAAA
Found at i:7627 original size:18 final size:18
Alignment explanation
Indices: 7600--7638 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
7590 TCAAGGGTAT
* *
7600 TTTCAGCCTTTCTTCATA
1 TTTCAACCTTTATTCATA
7618 TTTCAACCTTTATTCATA
1 TTTCAACCTTTATTCATA
7636 TTT
1 TTT
7639 ATTTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.23, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTCAACCTTTATTCATA
Found at i:7835 original size:118 final size:117
Alignment explanation
Indices: 7623--7850 Score: 341
Period size: 118 Copynumber: 1.9 Consensus size: 117
7613 TCATATTTCA
* * *
7623 ACCTTTATTCATATTTATTTATTTTTAATTAAGATAATTTTAAAAATGCATTTTTTAAATAAATT
1 ACCTTTAATCATATTTATTTATTTTTAATTAAGATAATTTTAAAAATACATTTTTAAAATAAATT
** * *
7688 TGTTACATTTAAGATTTTACTTATGAAGTATCTTTTATAAGGTTCCAACTCG
66 TAATACATTCAAGATTTTACTTATAAAGTATCTTTTATAAGGTTCCAACTCG
** *
7740 ACCTTTAATCATATTTATTTATTTTTTTGTTAAGATAA-TTTAAAACATATATTTTTAAAATAAA
1 ACCTTTAATCATATTTATTTA-TTTTTAATTAAGATAATTTTAAAA-ATACATTTTTAAAATAAA
7804 TTTAATACATTCAAGATTTTACTTATAAAGTATCTTTTATAAGGTTC
64 TTTAATACATTCAAGATTTTACTTATAAAGTATCTTTTATAAGGTTC
7851 AAACCCACAT
Statistics
Matches: 99, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
117 27 0.27
118 72 0.73
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.49
Consensus pattern (117 bp):
ACCTTTAATCATATTTATTTATTTTTAATTAAGATAATTTTAAAAATACATTTTTAAAATAAATT
TAATACATTCAAGATTTTACTTATAAAGTATCTTTTATAAGGTTCCAACTCG
Found at i:8495 original size:23 final size:21
Alignment explanation
Indices: 8469--8513 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
8459 TAGACTTGAT
8469 TTTATTGATTATTTATTATAAAA
1 TTTATT-ATTATTT-TTATAAAA
* *
8492 TTTATTTTTATTTTTTTAAAA
1 TTTATTATTATTTTTATAAAA
8513 T
1 T
8514 AGAAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 6 0.30
23 6 0.30
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTATTATTATTTTTATAAAA
Found at i:21013 original size:17 final size:18
Alignment explanation
Indices: 20985--21018 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
20975 CAAAATTGAT
20985 TTTTATAAAAATATTTTA
1 TTTTATAAAAATATTTTA
21003 TTTTA-AAAAATATTTT
1 TTTTATAAAAATATTTT
21019 CTAATATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTATAAAAATATTTTA
Done.