Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009453.1 Hibiscus syriacus cultivar Beakdansim tig00113685_pilon, 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: 44358
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Found at i:1821 original size:27 final size:29
Alignment explanation
Indices: 1763--1821 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
1753 TTTAATTTAC
*
1763 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
1792 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
1819 TTA
1 TTA
1822 ATCATATCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:11273 original size:27 final size:29
Alignment explanation
Indices: 11215--11273 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
11205 ATTTCTATAC
*
11215 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
11244 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
11271 TTA
1 TTA
11274 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:13641 original size:27 final size:29
Alignment explanation
Indices: 13583--13641 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
13573 ATTTCTGTAC
*
13583 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
13612 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
13639 TTA
1 TTA
13642 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:16016 original size:27 final size:29
Alignment explanation
Indices: 15958--16016 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
15948 ATTTCTGTAC
*
15958 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
15987 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
16014 TTA
1 TTA
16017 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:18383 original size:27 final size:29
Alignment explanation
Indices: 18325--18383 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
18315 ATTTATGTAC
*
18325 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
18354 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
18381 TTA
1 TTA
18384 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:20754 original size:27 final size:29
Alignment explanation
Indices: 20696--20754 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
20686 ATTTATGTAC
*
20696 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
20725 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
20752 TTA
1 TTA
20755 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:32367 original size:27 final size:29
Alignment explanation
Indices: 32309--32367 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
32299 ATTTCTGTAC
*
32309 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
32338 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
32365 TTA
1 TTA
32368 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:34738 original size:27 final size:29
Alignment explanation
Indices: 34680--34738 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
34670 ATTTCTGTAC
*
34680 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
34709 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
34736 TTA
1 TTA
34739 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:37108 original size:27 final size:29
Alignment explanation
Indices: 37050--37108 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
37040 ATTTCTGTAC
*
37050 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
37079 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
37106 TTA
1 TTA
37109 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:41847 original size:27 final size:29
Alignment explanation
Indices: 41789--41847 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
41779 ATTTCTGTAC
*
41789 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
41818 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
41845 TTA
1 TTA
41848 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Done.