Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007601.1 Hibiscus syriacus cultivar Beakdansim tig00022001_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: 32409
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Found at i:10941 original size:33 final size:32
Alignment explanation
Indices: 10904--10992 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 32
10894 GCGTGAGCCC
*
10904 CGGTCACCATCGGCAATCCCAGGCGGGTGGCCT
1 CGGTCACCATCGGCAAACCCAGGCGGGT-GCCT
* ** *
10937 CGGTCACCATCGGCAAAACCATACGGGTGTCT
1 CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
*
10969 CGGTCACCATCGGCAACCCCAGGC
1 CGGTCACCATCGGCAAACCCAGGC
10993 CATTGGTGAG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 23 0.49
33 24 0.51
ACGTcount: A:0.20, C:0.37, G:0.28, T:0.15
Consensus pattern (32 bp):
CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
Found at i:11080 original size:32 final size:32
Alignment explanation
Indices: 11039--11170 Score: 205
Period size: 32 Copynumber: 4.2 Consensus size: 32
11029 GTGCGTGAGG
* *
11039 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
11071 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
11103 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* *
11135 CTCGGTCACCATCGGC-AACCCCGACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
11166 CTCGG
1 CTCGG
11171 CAACCCCAGG
Statistics
Matches: 95, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
31 18 0.19
32 65 0.68
33 12 0.13
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.14
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:11295 original size:31 final size:31
Alignment explanation
Indices: 11254--11351 Score: 92
Period size: 31 Copynumber: 3.1 Consensus size: 31
11244 CAACCCCCGA
11254 CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
1 CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
* * * ****
11285 CGGGGGCCTCGGTC-ACCATC-GGCAACCCCCG
1 CGGGTGCCTCGG-CAACC-CCAGGCCACGGGTG
11316 ACGGGTGCCTCGGCAACCCCAGGCCACGGGTG
1 -CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
11348 CGGG
1 CGGG
11352 AGTGCCGCAC
Statistics
Matches: 48, Mismatches: 14, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
31 26 0.54
32 22 0.46
ACGTcount: A:0.13, C:0.40, G:0.38, T:0.09
Consensus pattern (31 bp):
CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
Found at i:11316 original size:63 final size:63
Alignment explanation
Indices: 11217--11351 Score: 261
Period size: 63 Copynumber: 2.1 Consensus size: 63
11207 GCCGAGAGTT
*
11217 GGGTGCGGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
11280 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
11343 GGGTGCGGG
1 GGGTGCGGG
11352 AGTGCCGCAC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.13, C:0.39, G:0.37, T:0.10
Consensus pattern (63 bp):
GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
Found at i:11316 original size:158 final size:157
Alignment explanation
Indices: 11135--11423 Score: 449
Period size: 158 Copynumber: 1.8 Consensus size: 157
11125 AGACGGGTGT
* *
11135 CTCGGTCACCATCGGCAACCCCGACGGGTGGCTCGGCAACCCCAGGCCACGGGTGCGGGAGTTCC
1 CTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCC
* * *
11200 GGACAGAGCCGAGAGTTGGGTGCG-G-GGTCCTCGGTCACCATCGGCAACCCCCGACGGGT-GCC
66 GCACAGAACCGAGAGTT-GGTGCGTGAGG--CTCGGTCACCATCGGCAACCCCAGACGGGTGGCC
11262 TCGGCAACCCCAGGCCACGGGTGCGGGGGC
128 TCGGCAACCCCAGGCCACGGGTGCGGGGGC
11292 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
1 CTCGGTCACCATCGGCAA-CCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
* * *
11357 CGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTC
65 CGCACAGAACCGAGAGTTGGTGCGTGAGGCTCGGTCACCATCGGCAACCCCAGACGGGTGGCCTC
11422 GG
130 GG
11424 TCACCATTGG
Statistics
Matches: 120, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
157 51 0.43
158 67 0.56
159 2 0.02
ACGTcount: A:0.16, C:0.36, G:0.37, T:0.12
Consensus pattern (157 bp):
CTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCC
GCACAGAACCGAGAGTTGGTGCGTGAGGCTCGGTCACCATCGGCAACCCCAGACGGGTGGCCTCG
GCAACCCCAGGCCACGGGTGCGGGGGC
Found at i:11327 original size:95 final size:93
Alignment explanation
Indices: 11103--11328 Score: 233
Period size: 95 Copynumber: 2.4 Consensus size: 93
11093 AGACGGGTGT
* *
11103 CTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGACGGGTGGCT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCCGACGGGTGCCT
11168 CGGCAACCCCAGGCCACGGGTGCGGGAG
66 CGGCAACCCCAGGCCACGGGTGCGGGAG
* * * * * ***** *
11196 TTCCGGACA-GAGCCG-AGAGTTGGGTGCGGG-GTCCTCGGTCACCATCGGCAACCCCCGACGGG
1 CT-CGGTCACCATCGGCA-AACCCAG-ACGGGTG-CCTCGGTCACCATCGGCAA-CCCCGACGGG
*
11258 TGCCTCGGCAACCCCAGGCCACGGGTGCGGGGG
61 TGCCTCGGCAACCCCAGGCCACGGGTGCGGGAG
* *
11291 CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
1 -CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGG
11329 CAACCCCAGG
Statistics
Matches: 99, Mismatches: 25, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
92 1 0.01
93 7 0.07
94 27 0.27
95 56 0.57
96 7 0.07
97 1 0.01
ACGTcount: A:0.16, C:0.37, G:0.35, T:0.12
Consensus pattern (93 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCCGACGGGTGCCT
CGGCAACCCCAGGCCACGGGTGCGGGAG
Found at i:11460 original size:32 final size:32
Alignment explanation
Indices: 11386--11519 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
11376 GTGCGTGAGG
* *
11386 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
11419 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
11451 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
* *
11483 CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
11515 CTCGG
1 CTCGG
11520 CAACCCCAGG
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
32 65 0.71
33 26 0.29
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.16
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:11602 original size:95 final size:95
Alignment explanation
Indices: 11280--11668 Score: 369
Period size: 95 Copynumber: 4.1 Consensus size: 95
11270 CCCAGGCCAC
11280 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
*
11345 GTGCGGGAGTGCCGCACAGAACCGAGCG-T
66 GTGCGGGAGTGCCGCACAGAACCGAGAGCT
* * * * * *** *
11374 TGGTGCGTGAGG-CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTC-ACCATTGGCAA
1 GGGTGCG-GGGGCCTCGGTCACCATCGGCAACCCCCGACGGGT-GCCTCGG-CAACCCCAGGCCA
* *** * * * * * *
11437 AGCCAGACGGGTGT-CTCGGTCAC-CATCGGCA-AACC
63 CGGGTG-CGGGAGTGC-C-G-CACAGAACCG-AGAGCT
** * * *
11472 CAG-ACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
* *
11536 GTGCGGGAGTGCCGCACAGAGCCGAGAGTT
66 GTGCGGGAGTGCCGCACAGAACCGAGAGCT
* * **
11566 GGGTGCGGGGGCCTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGTCCATTG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
*
11631 GTGCGGGAGTGCCGCACAGAACCGAGCGCT
66 GTGCGGGAGTGCCGCACAGAACCGAGAGCT
11661 GGGTGCGG
1 GGGTGCGG
11669 CAGCCTCGCA
Statistics
Matches: 225, Mismatches: 55, Indels: 29
0.73 0.18 0.09
Matches are distributed among these distances:
93 4 0.02
94 39 0.17
95 117 0.52
96 27 0.12
97 33 0.15
98 5 0.02
ACGTcount: A:0.17, C:0.34, G:0.36, T:0.13
Consensus pattern (95 bp):
GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
GTGCGGGAGTGCCGCACAGAACCGAGAGCT
Found at i:25426 original size:33 final size:31
Alignment explanation
Indices: 25389--25476 Score: 104
Period size: 31 Copynumber: 2.7 Consensus size: 31
25379 GCGTGAGCCC
25389 CGGTCACCATCGGCAATCCCAGGCGGGTGGCCT
1 CGGTCACCATCGGCAA-CCCAGGCGGGT-GCCT
** ** *
25422 CGGTCACCATCGGCAAAACATACGGGTGTCT
1 CGGTCACCATCGGCAACCCAGGCGGGTGCCT
25453 CGGTCACCATCGGCAACCCCAGGC
1 CGGTCACCATCGGCAA-CCCAGGC
25477 CATTGGTGAG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
31 19 0.42
32 10 0.22
33 16 0.36
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.15
Consensus pattern (31 bp):
CGGTCACCATCGGCAACCCAGGCGGGTGCCT
Found at i:25601 original size:32 final size:32
Alignment explanation
Indices: 25522--25651 Score: 178
Period size: 32 Copynumber: 4.2 Consensus size: 32
25512 GTGCGTGAGG
* *
25522 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
25554 CTCGGT---CATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
25583 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* * *
25615 CTCGGTCACCATCGGCAACCCCCGACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
25647 CTCGG
1 CTCGG
25652 CAACCCCAGG
Statistics
Matches: 89, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
29 14 0.16
30 12 0.13
32 63 0.71
ACGTcount: A:0.18, C:0.36, G:0.32, T:0.15
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:25816 original size:62 final size:62
Alignment explanation
Indices: 25698--25830 Score: 225
Period size: 63 Copynumber: 2.1 Consensus size: 62
25688 GCCGAGAGTT
*
25698 GGGTGCGGGGTCCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
25760 GGGGTGCGGGGGCCTCGGTCA-CATCGGCAACCCCCGACGGGTG-CTCGGCAACCCCAGGCCAC
1 -GGGTGCGGGGGCCTCGGTCACCATCGGCAA-CCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
25822 GGGTGCGGG
1 GGGTGCGGG
25831 AGTGCCGCAC
Statistics
Matches: 68, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
61 9 0.13
62 28 0.41
63 31 0.46
ACGTcount: A:0.14, C:0.38, G:0.38, T:0.11
Consensus pattern (62 bp):
GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
Found at i:25904 original size:32 final size:32
Alignment explanation
Indices: 25863--25996 Score: 180
Period size: 32 Copynumber: 4.2 Consensus size: 32
25853 TGGTGCGTGA
* *
25863 GGCTCGGTCACCATCGGCAATCCCAGGCGGGT
1 GGCTCGGTCACCATCGGCAAACCCAGACGGGT
* *
25895 GGCTCGGTCACCATTGGCAAAGCCAGACGGGT
1 GGCTCGGTCACCATCGGCAAACCCAGACGGGT
*
25927 GTCTCGGTCACCATCGGCAAACCCAGA-GGGT
1 GGCTCGGTCACCATCGGCAAACCCAGACGGGT
* * *
25958 GTCTCGGTCACCATCGGCAACCCCCGACGGGT
1 GGCTCGGTCACCATCGGCAAACCCAGACGGGT
*
25990 GCCTCGG
1 GGCTCGG
25997 CAACCCCAGG
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 29 0.32
32 62 0.68
ACGTcount: A:0.18, C:0.34, G:0.32, T:0.16
Consensus pattern (32 bp):
GGCTCGGTCACCATCGGCAAACCCAGACGGGT
Found at i:25933 original size:156 final size:156
Alignment explanation
Indices: 25560--25964 Score: 489
Period size: 156 Copynumber: 2.6 Consensus size: 156
25550 TGGCCTCGGT
* * *
25560 CATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACC
1 CATCGGC-AACCCAGACGGGTGCCTCGGTCACCATAGGCAAAGCCAGACGGGTGTCTCGGTCACC
* * *
25625 ATCGGCAACCCCCGACGGGTGGCTCGGCAACCCCAGGCCACGGGTGCGGGAGTTCCGGACAGAGC
65 ATCGGCAACCCCCGACGGGT-GCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAAC
25690 CGAGAGTTGGGTGCGGGGTCCTCGGTCAC
129 CGAGAGTTGGGTGCGGGG-CCTCGGTCAC
* ** * * ** * * *
25719 CATCGGCAACCCCGACGGGTGCCTCGG-CAACCCCAGGCCACG-GGGTGCGGGGGCCTCGGTCA-
1 CATCGGCAACCCAGACGGGTGCCTCGGTC-ACCATAGGCAAAGCCAG-ACGGGTGTCTCGGTCAC
25781 CATCGGCAACCCCCGACGGGTGCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAAC
64 CATCGGCAACCCCCGACGGGTGCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAAC
*
25846 CGAGCGTT-GGTGCGTGAGG-CTCGGTCAC
129 CGAGAGTTGGGTGCG-G-GGCCTCGGTCAC
* * *
25874 CATCGGCAATCCCAGGCGGGTGGCTCGGTCACCATTGGCAAAGCCAGACGGGTGTCTCGGTCACC
1 CATCGGCAA-CCCAGACGGGTGCCTCGGTCACCATAGGCAAAGCCAGACGGGTGTCTCGGTCACC
* *
25939 ATCGGCAAACCCAGA-GGGTGTCTCGG
65 ATCGGCAACCCCCGACGGGTG-CTCGG
25965 TCACCATCGG
Statistics
Matches: 205, Mismatches: 32, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
155 24 0.12
156 90 0.44
157 46 0.22
158 38 0.19
159 7 0.03
ACGTcount: A:0.18, C:0.34, G:0.35, T:0.13
Consensus pattern (156 bp):
CATCGGCAACCCAGACGGGTGCCTCGGTCACCATAGGCAAAGCCAGACGGGTGTCTCGGTCACCA
TCGGCAACCCCCGACGGGTGCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAACCG
AGAGTTGGGTGCGGGGCCTCGGTCAC
Found at i:25987 original size:63 final size:64
Alignment explanation
Indices: 25865--25996 Score: 185
Period size: 63 Copynumber: 2.1 Consensus size: 64
25855 GTGCGTGAGG
* * * * *
25865 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGGAGGGTGGCTCGGTCACCATCGGCAAACCCAGACGGGTGC
* * *
25929 CTCGGTCACCATCGGCAAACCCA-GAGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGGAGGGTGGCTCGGTCACCATCGGCAAACCCAGACGGGTGC
25992 CTCGG
1 CTCGG
25997 CAACCCCAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
63 38 0.63
64 22 0.37
ACGTcount: A:0.18, C:0.35, G:0.31, T:0.16
Consensus pattern (64 bp):
CTCGGTCACCATCGGCAAACCCAGGAGGGTGGCTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:26147 original size:92 final size:93
Alignment explanation
Indices: 25960--26148 Score: 267
Period size: 92 Copynumber: 2.0 Consensus size: 93
25950 CAGAGGGTGT
*
25960 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
1 CTCGGTCACCATCGGCAACCACCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
* **
26025 CGCACAGAGCGAGAGTTGGGGCGGGGGC
66 CGCACAGACCGAGAGTTGGGGCGGCAGC
* **
26053 CTCGGTCACCATCGGCAA-CACCGACGGGTGCCTCGGCAA-CCCAGTCCATTGGTGCGGGAGTGC
1 CTCGGTCACCATCGGCAACCACCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
*
26116 CGCACAGAACCGAGCG-TGGGCGCGGCAGC
66 CGCACAG-ACCGAGAGTTGGG-GCGGCAGC
26145 CTCG
1 CTCG
26149 CACAGCGTCG
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
91 32 0.37
92 36 0.42
93 18 0.21
ACGTcount: A:0.17, C:0.35, G:0.37, T:0.11
Consensus pattern (93 bp):
CTCGGTCACCATCGGCAACCACCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
CGCACAGACCGAGAGTTGGGGCGGCAGC
Done.