Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004187.1 Hibiscus syriacus cultivar Beakdansim tig00009159_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: 49347
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3609 original size:22 final size:22
Alignment explanation
Indices: 3573--3614 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3563 AAGAAAGTGA
3573 AGCACTCAAAAGAGAGAAAAACC
1 AGCACTCAAAAGAGA-AAAAACC
3596 AGCACTC-AAAGAGAAAAAA
1 AGCACTCAAAAGAGAAAAAA
3615 GCAAAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.60, C:0.19, G:0.17, T:0.05
Consensus pattern (22 bp):
AGCACTCAAAAGAGAAAAAACC
Found at i:14927 original size:7 final size:7
Alignment explanation
Indices: 14915--14940 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
14905 ACAAAACCCT
14915 AATAAAG
1 AATAAAG
14922 AATAAAG
1 AATAAAG
14929 AATAAAG
1 AATAAAG
14936 AATAA
1 AATAA
14941 CGAAACATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (7 bp):
AATAAAG
Found at i:23961 original size:35 final size:35
Alignment explanation
Indices: 23917--24015 Score: 153
Period size: 35 Copynumber: 2.8 Consensus size: 35
23907 ATAAGGGGAT
*
23917 GGTGATGATATAGGCATGAAATGGTGATAGAAGAA
1 GGTGATGATATAGGCGTGAAATGGTGATAGAAGAA
* * *
23952 GGTGATGATATAGGCGTGCAATGGTGATGGAAGAT
1 GGTGATGATATAGGCGTGAAATGGTGATAGAAGAA
23987 GGTGATGATATAGGCGTGAAAATGGTGAT
1 GGTGATGATATAGGCGTG-AAATGGTGAT
24016 GAAAGATGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
35 49 0.84
36 9 0.16
ACGTcount: A:0.33, C:0.04, G:0.37, T:0.25
Consensus pattern (35 bp):
GGTGATGATATAGGCGTGAAATGGTGATAGAAGAA
Found at i:25245 original size:22 final size:22
Alignment explanation
Indices: 25219--25287 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
25209 ATAGTATATT
25219 TTAATAACTTATATCTCACATA
1 TTAATAACTTATATCTCACATA
* * * *
25241 TTAATGGA-TAAGT-TATCA-ACA
1 TTAAT-AACTTA-TATCTCACATA
25262 -TAATAACTTATATCTCACATA
1 TTAATAACTTATATCTCACATA
25283 TTAAT
1 TTAAT
25288 GGATAAGTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
19 2 0.06
20 10 0.30
21 4 0.12
22 15 0.45
23 2 0.06
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.39
Consensus pattern (22 bp):
TTAATAACTTATATCTCACATA
Found at i:25267 original size:42 final size:42
Alignment explanation
Indices: 25220--25311 Score: 184
Period size: 42 Copynumber: 2.2 Consensus size: 42
25210 TAGTATATTT
25220 TAATAACTTATATCTCACATATTAATGGATAAGTTATCAACA
1 TAATAACTTATATCTCACATATTAATGGATAAGTTATCAACA
25262 TAATAACTTATATCTCACATATTAATGGATAAGTTATCAACA
1 TAATAACTTATATCTCACATATTAATGGATAAGTTATCAACA
25304 TAATAACT
1 TAATAACT
25312 ATAGGTATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (42 bp):
TAATAACTTATATCTCACATATTAATGGATAAGTTATCAACA
Found at i:35521 original size:32 final size:30
Alignment explanation
Indices: 35451--35522 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 30
35441 CCTGGCTTGC
* *
35451 TTTCTTTTTTTGACTTTTCTTCTTTTTCTT
1 TTTCTTTTTCTGAATTTTCTTCTTTTTCTT
* *
35481 TTCCCTTTTTCTGAATTTTCATTCTTTTTGTAT
1 TT-TCTTTTTCTGAATTTTC-TTCTTTTTCT-T
35514 TTTCTTTTT
1 TTTCTTTTT
35523 TAACTCTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 2 0.06
31 14 0.41
32 15 0.44
33 3 0.09
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.72
Consensus pattern (30 bp):
TTTCTTTTTCTGAATTTTCTTCTTTTTCTT
Found at i:43192 original size:13 final size:13
Alignment explanation
Indices: 43174--43204 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
43164 CTCTAGCTAG
43174 CTCAAATGTCCAA
1 CTCAAATGTCCAA
*
43187 CTCAAATGTCCAG
1 CTCAAATGTCCAA
43200 CTCAA
1 CTCAA
43205 GTCAACTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.32, G:0.10, T:0.23
Consensus pattern (13 bp):
CTCAAATGTCCAA
Found at i:44255 original size:18 final size:18
Alignment explanation
Indices: 44232--44280 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
44222 ATTTCTATGG
44232 TGGATGTTTAATGGGAGT
1 TGGATGTTTAATGGGAGT
44250 TGGATGTTTAATGGGAGT
1 TGGATGTTTAATGGGAGT
* *
44268 TGGTTGCTTAATG
1 TGGATGTTTAATG
44281 ATGGATAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.20, C:0.02, G:0.37, T:0.41
Consensus pattern (18 bp):
TGGATGTTTAATGGGAGT
Found at i:44692 original size:36 final size:37
Alignment explanation
Indices: 44625--44697 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
44615 CATCTTCAAA
*
44625 AAGCTTTTCTTCATTTGAATTTTTCCTCTAAATGTTC
1 AAGCTTTTCTTCATTTGAATTTTTCCTCTAAACGTTC
44662 AAGCTTTTCTTCATTTGAA-TTTTCCTCTAAACGTTC
1 AAGCTTTTCTTCATTTGAATTTTTCCTCTAAACGTTC
44698 TCCTTCAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 16 0.46
37 19 0.54
ACGTcount: A:0.22, C:0.21, G:0.08, T:0.49
Consensus pattern (37 bp):
AAGCTTTTCTTCATTTGAATTTTTCCTCTAAACGTTC
Found at i:46004 original size:21 final size:21
Alignment explanation
Indices: 45978--46022 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
45968 TAAAACACCT
45978 GATGTCTCTTGATCATTCAGG
1 GATGTCTCTTGATCATTCAGG
45999 GATGTCTCTTGATCATTCAGG
1 GATGTCTCTTGATCATTCAGG
46020 GAT
1 GAT
46023 ATCTTTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (21 bp):
GATGTCTCTTGATCATTCAGG
Done.