Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009486.1 Hibiscus syriacus cultivar Beakdansim tig00114569_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: 8052
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Found at i:5052 original size:29 final size:31
Alignment explanation
Indices: 5011--5139 Score: 138
Period size: 31 Copynumber: 4.2 Consensus size: 31
5001 CCTGGGGTTG
5011 CCGAG-CACCCGTC-GGGGT-CCGATGGTGA
1 CCGAGACACCCGTCTGGGGTGCCGATGGTGA
**
5039 CCGAGACACCCGTCTGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGGTGCCGATGGTGA
** *
5070 CCGAGACACCCGTCTGGCTTTGCCAATGGTGA
1 CCGAGACACCCGTCTGG-GGTGCCGATGGTGA
* * *
5102 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGG-GTGCCGATGGTGA
5135 CCGAG
1 CCGAG
5140 CCTCACGCAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
28 5 0.06
29 8 0.09
30 3 0.03
31 27 0.31
32 18 0.20
33 27 0.31
ACGTcount: A:0.16, C:0.32, G:0.34, T:0.18
Consensus pattern (31 bp):
CCGAGACACCCGTCTGGGGTGCCGATGGTGA
Found at i:5067 original size:31 final size:31
Alignment explanation
Indices: 5029--5139 Score: 159
Period size: 31 Copynumber: 3.5 Consensus size: 31
5019 CCGTCGGGGT
5029 CCGATGGTGACCGAGACACCCGTCTGGTTTG
1 CCGATGGTGACCGAGACACCCGTCTGGTTTG
5060 CCGATGGTGACCGAGACACCCGTCTGGCTTTG
1 CCGATGGTGACCGAGACACCCGTCTGG-TTTG
* * * *
5092 CCAATGGTGACCGAGGCCACCCGCCTGGGATTG
1 CCGATGGTGACCGA-GACACCCGTCT-GGTTTG
5125 CCGATGGTGACCGAG
1 CCGATGGTGACCGAG
5140 CCTCACGCAC
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.38
32 18 0.25
33 25 0.35
34 2 0.03
ACGTcount: A:0.17, C:0.31, G:0.33, T:0.19
Consensus pattern (31 bp):
CCGATGGTGACCGAGACACCCGTCTGGTTTG
Found at i:5126 original size:33 final size:32
Alignment explanation
Indices: 5029--5139 Score: 161
Period size: 33 Copynumber: 3.5 Consensus size: 32
5019 CCGTCGGGGT
5029 CCGATGGTGACCGAGACACCCGTCT-GGTTTG
1 CCGATGGTGACCGAGACACCCGTCTGGGTTTG
*
5060 CCGATGGTGACCGAGACACCCGTCTGGCTTTG
1 CCGATGGTGACCGAGACACCCGTCTGGGTTTG
* * * *
5092 CCAATGGTGACCGAGGCCACCCGCCTGGGATTG
1 CCGATGGTGACCGA-GACACCCGTCTGGGTTTG
5125 CCGATGGTGACCGAG
1 CCGATGGTGACCGAG
5140 CCTCACGCAC
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
31 25 0.35
32 19 0.27
33 27 0.38
ACGTcount: A:0.17, C:0.31, G:0.33, T:0.19
Consensus pattern (32 bp):
CCGATGGTGACCGAGACACCCGTCTGGGTTTG
Found at i:5267 original size:23 final size:21
Alignment explanation
Indices: 5237--5280 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5227 CGAGGCCCCC
5237 GCACCCGTGGCCTGGGTTGCCGA
1 GCACCCGT--CCTGGGTTGCCGA
*
5260 GCACCCGTCGTGGGTTGCCGA
1 GCACCCGTCCTGGGTTGCCGA
5281 TGGTGACCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
23 8 0.40
ACGTcount: A:0.09, C:0.34, G:0.39, T:0.18
Consensus pattern (21 bp):
GCACCCGTCCTGGGTTGCCGA
Found at i:5267 original size:185 final size:185
Alignment explanation
Indices: 4936--5292 Score: 446
Period size: 185 Copynumber: 1.9 Consensus size: 185
4926 CCCGTCGGTG
* *
4936 TTGCCGATGGTGACCGAGGCCCCCGCACCCAACTCTCGCTCTGTGCGGCACTCCCGCACCCGTGG
1 TTGCCGATGGTGACCGAGGCCCACGCACCCAACGCTCGCTCTGTGCGGCACTCCCGCACCCGTGG
* ** *
5001 CCTGGGGTTGCCGAGCACCCGTCGGGGTCCGATGGTGACCGAGACACCCGTCTGGTTTGCCGATG
66 CCTGGGGTTGCCGAGCACCCGTCGGGGTCCGATGGTGACCGAGACACCCGACCCGTTGGCCGA-G
*
5066 GTGACCGAGACACCCGTC-TGGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGA
130 GTGACCGAGACACCCGTCGTGG-GTTGCCAATGGTGACCGAGGCCACCCGCCTGGGA
*
5122 TTGCCGATGGTGACCGA-GCCTCACGCA-CCAACGCTCGGTTCT-TGCGGCACTCCCGCACCCGT
1 TTGCCGATGGTGACCGAGGCC-CACGCACCCAACGCTC-GCTCTGTGCGGCACTCCCGCACCCGT
* *
5184 GGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGAT-G-GACCGAGGCCCCCGCACCCG-TG
64 GGCCTGGGGTTGCCGA-GCACCCGTC-GGGG-T-CCGATGGTGACCGAGACACCCG-ACCCGTTG
*
5246 GCCTG-GGTTG-CCGAG-CACCCGTCGTGGGTTGCCGATGGTGACCGAGG
124 GCC-GAGG-TGACCGAGACACCCGTCGTGGGTTGCCAATGGTGACCGAGG
5293 ACCCCGCACC
Statistics
Matches: 150, Mismatches: 11, Indels: 21
0.82 0.06 0.12
Matches are distributed among these distances:
185 73 0.49
186 45 0.30
187 22 0.15
188 5 0.03
189 5 0.03
ACGTcount: A:0.13, C:0.36, G:0.34, T:0.17
Consensus pattern (185 bp):
TTGCCGATGGTGACCGAGGCCCACGCACCCAACGCTCGCTCTGTGCGGCACTCCCGCACCCGTGG
CCTGGGGTTGCCGAGCACCCGTCGGGGTCCGATGGTGACCGAGACACCCGACCCGTTGGCCGAGG
TGACCGAGACACCCGTCGTGGGTTGCCAATGGTGACCGAGGCCACCCGCCTGGGA
Found at i:5279 original size:59 final size:63
Alignment explanation
Indices: 5173--5303 Score: 216
Period size: 61 Copynumber: 2.1 Consensus size: 63
5163 TTGCGGCACT
*
5173 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGAT-G-GACCGAGGCC
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGAC
*
5234 CCCGCACCCGTGGCCT-GGGTTGCCGA-GCACCCGTCGTGGGTTGCCGATGGTGACCGAGGAC
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGAC
5295 CCCGCACCC
1 CCCGCACCC
5304 AACTCTCGCT
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
59 21 0.32
60 11 0.17
61 34 0.52
ACGTcount: A:0.11, C:0.38, G:0.37, T:0.14
Consensus pattern (63 bp):
CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGAC
Found at i:5291 original size:91 final size:91
Alignment explanation
Indices: 5196--5408 Score: 204
Period size: 93 Copynumber: 2.3 Consensus size: 91
5186 CCTGGGGTTG
* * *
5196 CCGAGGCACCCGTCGGGGGTTGCCGATGGACCGAGGCCCCCGCACCCGTGGCC-TGGGTTGCCGA
1 CCGAGGCACCCGTCCGGGCTTGCCGATGGACCGA-ACCCCCGCACCCGTGGCCGTGGGTTGCCGA
5260 G-CACCCGTCGTGGGTTGCCGATGGTGA
65 GCCACCCGTCG-GGGTTGCCGATGGTGA
* *** * *
5287 CCGAGG-ACCCCGCACCCAACTCTCGCTC--T-GTCCGAACTCCCGCACCCGTGGCCTGTGGGTT
1 CCGAGGCA-CCCG-TCCGGGCT-T-GC-CGATGGACCGAACCCCCGCACCCGTGGCC-GTGGGTT
5348 GCCGAGCCACCCGTCGGGGTTGCCGATGGTGA
60 GCCGAGCCACCCGTCGGGGTTGCCGATGGTGA
* * *
5380 CCGAGACACCCGTCTGGGTTTGCCGATGG
1 CCGAGGCACCCGTCCGGGCTTGCCGATGG
5409 TGACCGAGAC
Statistics
Matches: 94, Mismatches: 16, Indels: 23
0.71 0.12 0.17
Matches are distributed among these distances:
89 1 0.01
90 3 0.03
91 28 0.30
92 10 0.11
93 39 0.41
94 12 0.13
95 1 0.01
ACGTcount: A:0.12, C:0.36, G:0.35, T:0.17
Consensus pattern (91 bp):
CCGAGGCACCCGTCCGGGCTTGCCGATGGACCGAACCCCCGCACCCGTGGCCGTGGGTTGCCGAG
CCACCCGTCGGGGTTGCCGATGGTGA
Found at i:5408 original size:32 final size:32
Alignment explanation
Indices: 5349--5480 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
5339 CTGTGGGTTG
* *
5349 CCGAGCCACCCGTC-GGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
5380 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
**
5412 CCGAGACACCCGTCTGTTTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
5444 CCGAGGCCACCCGCCTGGG-TTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
5476 CCGAG
1 CCGAG
5481 CCTCACGCAC
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
31 14 0.15
32 67 0.74
33 10 0.11
ACGTcount: A:0.14, C:0.31, G:0.35, T:0.20
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Found at i:5455 original size:152 final size:151
Alignment explanation
Indices: 5039--5455 Score: 395
Period size: 152 Copynumber: 2.7 Consensus size: 151
5029 CCGATGGTGA
* * *
5039 CCGAGACACCCGTCTGGTTTGCCGATGGTGACCGAGACACCCGTCTGGCTTTGCCAATGGTGACC
1 CCGAGACACCCGTCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCC-ATGGTGACC
* * * * * *
5104 GAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCTTGCGG
65 GA-G-CACCCGTCTGTGATTGCCGATGGTGACCGAGGCGCA--C-CCAACGCTCGGCTCTTGCCG
*
5169 CACTCCCGCACCCGTGGCCTGGGGTTG
125 AACTCCCGCACCCGTGGCCTGGGGTTG
* * * *** *
5196 CCGAGGCACCCGTCGGGGGTTGCCGAT-G-GACCGAGGCCCCCG-CACCCG-TGGCC-TGGGTTG
1 CCGAGACACCCGTC-GGGGTTGCCGATGGTGACCGAGACACCCGTC-TGGGTTTGCCAT-GG-TG
* *
5256 -CCGAGCACCCGTC-GTGGGTTGCCGATGGTGACCGAGGACCCCGCACCCAACTCTC-GCTC-TG
62 ACCGAGCACCCGTCTGT-GATTGCCGATGGTGACCGAGG----CGCACCCAACGCTCGGCTCTTG
5317 TCCGAACTCCCGCACCCGTGGCCTGTGGGTTG
122 -CCGAACTCCCGCACCCGTGGCCTG-GGGTTG
*
5349 CCGAGCCACCCGTCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACC
1 CCGAGACACCCGTCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCC-ATGGTGACC
**
5414 GAGACACCCGTCTGTTTTTGCCGATGGTGACCGAGGC-CACCC
65 GAG-CACCCGTCTGTGATTGCCGATGGTGACCGAGGCGCACCC
5456 GCCTGGGTTG
Statistics
Matches: 212, Mismatches: 28, Indels: 45
0.74 0.10 0.16
Matches are distributed among these distances:
151 3 0.01
152 68 0.32
153 31 0.15
154 20 0.09
155 14 0.07
156 22 0.10
157 42 0.20
158 12 0.06
ACGTcount: A:0.14, C:0.35, G:0.33, T:0.18
Consensus pattern (151 bp):
CCGAGACACCCGTCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCATGGTGACCG
AGCACCCGTCTGTGATTGCCGATGGTGACCGAGGCGCACCCAACGCTCGGCTCTTGCCGAACTCC
CGCACCCGTGGCCTGGGGTTG
Found at i:5540 original size:341 final size:337
Alignment explanation
Indices: 4913--5540 Score: 1082
Period size: 342 Copynumber: 1.9 Consensus size: 337
4903 CAATGGACTG
* *
4913 GGGTTGCCGAGCACCCGTCGGTGTTGCCGATGGTGACCGAGGCCCCCGCACCCAACTCTCGCTCT
1 GGGTTGCCGAGCACCCGTCGGGGTTGCCGATGGTGACCGAGGACCCCGCACCCAACTCTCGCTCT
* *
4978 GTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCACCCGTCGGGGTCCGATGGTGACCGA
66 GTGCCGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCACCCGTCGGGGTCCGATGGTGACCGA
5043 GACACCCGTCTGGTTTGCCGATGGTGACCGAGACACCCGTCTGGCTTTGCCAATGGTGACCGAGG
131 GACACCCGTCTGGTTTGCCGATGGTGACCGAGACACCCGTCTGGCTTTGCCAATGGTGACCGAGG
5108 CCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCTTGCGGCACT
196 CCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCTTGCGGCACT
**
5173 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGACCGAGGCCCCCG
261 CCCGCACCAATGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGACCGAGGCCCCCG
5238 CACCCGTGGCCT
326 CACCCGTGGCCT
5250 GGGTTGCCGAGCACCCGTCGTGGGTTGCCGATGGTGACCGAGGACCCCGCACCCAACTCTCGCTC
1 GGGTTGCCGAGCACCCGTCG-GGGTTGCCGATGGTGACCGAGGACCCCGCACCCAACTCTCGCTC
5315 TGT-CCGAACTCCCGCACCCGTGGCCTGTGGGTTGCCGAGCCACCCGTCGGGGTTGCCGATGGTG
65 TGTGCCGAACTCCCGCACCCGTGGCCTG-GGGTTGCCGAG-CACCCGTCGGGG-T-CCGATGGTG
** *
5379 ACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCCGTCTGTTTTTGCCGATGGTGA
126 ACCGAGACACCCGTCT-GGTTTGCCGATGGTGACCGAGACACCCGTCTGGCTTTGCCAATGGTGA
5444 CCGAGGCCACCCGCCTGGG-TTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCTGTG
190 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCT-TG
*
5508 CGGCACTCCCTCACCAATGGCCT-GGGTTGCCGA
254 CGGCACTCCCGCACCAATGGCCTGGGGTTGCCGA
5541 TGGTGACCGA
Statistics
Matches: 274, Mismatches: 10, Indels: 10
0.93 0.03 0.03
Matches are distributed among these distances:
337 42 0.15
338 56 0.20
339 12 0.04
340 1 0.00
341 77 0.28
342 86 0.31
ACGTcount: A:0.13, C:0.36, G:0.33, T:0.18
Consensus pattern (337 bp):
GGGTTGCCGAGCACCCGTCGGGGTTGCCGATGGTGACCGAGGACCCCGCACCCAACTCTCGCTCT
GTGCCGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCACCCGTCGGGGTCCGATGGTGACCGA
GACACCCGTCTGGTTTGCCGATGGTGACCGAGACACCCGTCTGGCTTTGCCAATGGTGACCGAGG
CCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCTTGCGGCACT
CCCGCACCAATGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGACCGAGGCCCCCG
CACCCGTGGCCT
Done.