Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168057.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_307, 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: 36431
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:7031 original size:20 final size:22
Alignment explanation
Indices: 7000--7053 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
6990 CATTTTCTAA
7000 CAAAAAACATCTTA-AA-TAATC
1 CAAAAAA-ATCTTATAAGTAATC
7021 CAAAAAAATCTTATAAGTAATC
1 CAAAAAAATCTTATAAGTAATC
7043 CTAAAAAAATC
1 C-AAAAAAATC
7054 AAACTTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.20
21 9 0.30
22 6 0.20
23 9 0.30
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (22 bp):
CAAAAAAATCTTATAAGTAATC
Found at i:7635 original size:62 final size:62
Alignment explanation
Indices: 7493--7630 Score: 203
Period size: 62 Copynumber: 2.3 Consensus size: 62
7483 ACATTTTTTA
* * *
7493 TTAAGATATTTTTAAATCAAAAATATCTTAAATAATCTCCTGATATATTTTTAAAAAAATTAT
1 TTAAGATATTTTTAAATAAAAAACATCTTAAATAATCTCCT-ATATATTTTAAAAAAAATTAT
7556 TTAAGAT-TTTTTAAATAAAAAACA-CTTCAAATAATCTCCT-TATA-TTTAAAAAAAATTAT
1 TTAAGATATTTTTAAATAAAAAACATCTT-AAATAATCTCCTATATATTTTAAAAAAAATTAT
7615 TTAAGATATTTTTAAA
1 TTAAGATATTTTTAAA
7631 AATAATCTCT
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
59 21 0.30
60 12 0.17
61 3 0.04
62 27 0.39
63 7 0.10
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (62 bp):
TTAAGATATTTTTAAATAAAAAACATCTTAAATAATCTCCTATATATTTTAAAAAAAATTAT
Found at i:12221 original size:13 final size:13
Alignment explanation
Indices: 12193--12231 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
12183 ATCGATTTGA
*
12193 ATTTTTATT-AAC
1 ATTTTTATTAAAT
12205 ATTTTTATTAAAT
1 ATTTTTATTAAAT
*
12218 ATTTTTAATAAAT
1 ATTTTTATTAAAT
12231 A
1 A
12232 ACTCTGCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTTTTATTAAAT
Found at i:17976 original size:15 final size:14
Alignment explanation
Indices: 17956--17986 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
17946 AGCTTTCTCA
17956 TCTCTTTTTCTATTT
1 TCTCTTTTTCT-TTT
17971 TCTCTTTTTCTTTT
1 TCTCTTTTTCTTTT
17985 TC
1 TC
17987 AGGTTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (14 bp):
TCTCTTTTTCTTTT
Found at i:30042 original size:20 final size:20
Alignment explanation
Indices: 30016--30062 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
30006 TTTTTAGTTT
30016 ATTTTTAAATAAAATTTT-AA
1 ATTTTTAAA-AAAATTTTGAA
* *
30036 TTTTTTAAAAAAGTTTTGAA
1 ATTTTTAAAAAAATTTTGAA
30056 ATTTTTA
1 ATTTTTA
30063 TTTTTTTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
ATTTTTAAAAAAATTTTGAA
Found at i:32878 original size:20 final size:21
Alignment explanation
Indices: 32835--32879 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
32825 TATTTGAACG
32835 TTTG-TTTTTTTATTTTGATA
1 TTTGATTTTTTTATTTTGATA
* *
32855 TTTGATTTTTTTGTTTTTAT-
1 TTTGATTTTTTTATTTTGATA
32875 TTTGA
1 TTTGA
32880 AAATTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.13, C:0.00, G:0.11, T:0.76
Consensus pattern (21 bp):
TTTGATTTTTTTATTTTGATA
Found at i:34766 original size:7 final size:7
Alignment explanation
Indices: 34754--34778 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
34744 TAAAATCTTA
34754 ATTTATT
1 ATTTATT
34761 ATTTATT
1 ATTTATT
34768 ATTTATT
1 ATTTATT
34775 ATTT
1 ATTT
34779 TTTAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTATT
Found at i:35226 original size:3 final size:3
Alignment explanation
Indices: 35220--35244 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35210 TTTAGGTGGA
35220 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
35245 TTATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Done.