Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000345.1 Hibiscus syriacus cultivar Beakdansim tig00000636_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: 62630
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:19187 original size:14 final size:14
Alignment explanation
Indices: 19164--19224 Score: 60
Period size: 14 Copynumber: 4.7 Consensus size: 14
19154 GAACATAGAC
19164 GAACACAAACGAAT
1 GAACACAAACGAAT
*
19178 GAACATAAAC----
1 GAACACAAACGAAT
19188 GAACACAAACGAAT
1 GAACACAAACGAAT
*
19202 GAACATAAACGAA-
1 GAACACAAACGAAT
*
19215 CAACACAAAC
1 GAACACAAAC
19225 ACAAAAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
10 9 0.24
13 8 0.21
14 21 0.55
ACGTcount: A:0.59, C:0.23, G:0.11, T:0.07
Consensus pattern (14 bp):
GAACACAAACGAAT
Found at i:19189 original size:24 final size:24
Alignment explanation
Indices: 19154--19216 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
19144 AATGATAAAC
*
19154 GAACATAGACGAACACAAACGAAT
1 GAACATAAACGAACACAAACGAAT
19178 GAACATAAACGAACACAAACGAAT
1 GAACATAAACGAACACAAACGAAT
19202 GAACATAAACGAACA
1 GAACATAAACGAACA
19217 ACACAAACAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.57, C:0.21, G:0.14, T:0.08
Consensus pattern (24 bp):
GAACATAAACGAACACAAACGAAT
Found at i:20293 original size:2 final size:2
Alignment explanation
Indices: 20286--20316 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20276 GCCAAAATCC
20286 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
20317 AGACACAGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:38338 original size:29 final size:29
Alignment explanation
Indices: 38291--38346 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
38281 TTCACCTAAT
38291 TAAATTGATGTAGGCAATGACATCAAAAC
1 TAAATTGATGTAGGCAATGACATCAAAAC
38320 TAAATTGATGTAAGG-AATGACATCAAA
1 TAAATTGATGT-AGGCAATGACATCAAA
38347 TTAATTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (29 bp):
TAAATTGATGTAGGCAATGACATCAAAAC
Found at i:43733 original size:30 final size:30
Alignment explanation
Indices: 43697--43753 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
43687 GTTAAACATA
*
43697 TAGTTTACTCTTATTTGTTTTTCCAACTTG
1 TAGTTTACTCTTATTTGTTTATCCAACTTG
43727 TAGTTTACTCTTATTTGTTTATCCAAC
1 TAGTTTACTCTTATTTGTTTATCCAAC
43754 GTAACACGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.18, G:0.09, T:0.54
Consensus pattern (30 bp):
TAGTTTACTCTTATTTGTTTATCCAACTTG
Found at i:51134 original size:20 final size:21
Alignment explanation
Indices: 51109--51150 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
51099 CCAACTTCCA
51109 ATGCATTATG-AACCATTATT
1 ATGCATTATGCAACCATTATT
*
51129 ATGCATTATGCAACTATTATT
1 ATGCATTATGCAACCATTATT
51150 A
1 A
51151 GTTGCATGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
ATGCATTATGCAACCATTATT
Done.