Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007607.1 Hibiscus syriacus cultivar Beakdansim tig00022354_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: 39214
ACGTcount: A:0.23, C:0.26, G:0.29, T:0.21
Found at i:4559 original size:33 final size:32
Alignment explanation
Indices: 4522--4610 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 32
4512 GCGTGAGCCC
*
4522 CGGTCACCATCGGCAATCCCAGGCGGGTGGCCT
1 CGGTCACCATCGGCAAACCCAGGCGGGT-GCCT
* ** *
4555 CGGTCACCATCGGCAAAACCATACGGGTGTCT
1 CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
*
4587 CGGTCACCATCGGCAACCCCAGGC
1 CGGTCACCATCGGCAAACCCAGGC
4611 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:4749 original size:32 final size:31
Alignment explanation
Indices: 4656--4783 Score: 172
Period size: 30 Copynumber: 4.2 Consensus size: 31
4646 GGTGCGTGGG
* * *
4656 CTCGGTCACCATCGGCAACCCAGGCGTG-GC
1 CTCGGTCACCATCGGCAACCCAGACGGGTGT
4686 CTCGGTCACCATCGGCAAACCC--ACGGGTGT
1 CTCGGTCACCATCGGC-AACCCAGACGGGTGT
4716 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGC-AACCCAGACGGGTGT
* *
4748 CTCGGTCACCATCGGCAACCCCGACGGGTGG
1 CTCGGTCACCATCGGCAACCCAGACGGGTGT
4779 CTCGG
1 CTCGG
4784 CAACCCCAGG
Statistics
Matches: 89, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
29 3 0.03
30 39 0.44
31 23 0.26
32 24 0.27
ACGTcount: A:0.18, C:0.38, G:0.30, T:0.15
Consensus pattern (31 bp):
CTCGGTCACCATCGGCAACCCAGACGGGTGT
Found at i:4894 original size:58 final size:60
Alignment explanation
Indices: 4829--4955 Score: 222
Period size: 58 Copynumber: 2.1 Consensus size: 60
4819 GCCGAGAGTT
*
4829 GGTGCGGGTCCTCGGTCACCATCGGCAACCCCCGACGGTGCCTCGGC-ACCCCA-CCACG
1 GGTGCGGGGCCTCGGTCACCATCGGCAACCCCCGACGGTGCCTCGGCAACCCCAGCCACG
4887 GGTGCGGGGCCTCGGTCACCATCGGCAACCCCCGACGGTGCCTCGGCAACCCCAGGCCACG
1 GGTGCGGGGCCTCGGTCACCATCGGCAACCCCCGACGGTGCCTCGGCAACCCCA-GCCACG
4948 GGTGCGGG
1 GGTGCGGG
4956 AGTGCCGCAC
Statistics
Matches: 65, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
58 46 0.71
59 6 0.09
61 13 0.20
ACGTcount: A:0.13, C:0.42, G:0.34, T:0.11
Consensus pattern (60 bp):
GGTGCGGGGCCTCGGTCACCATCGGCAACCCCCGACGGTGCCTCGGCAACCCCAGCCACG
Found at i:5033 original size:149 final size:146
Alignment explanation
Indices: 4748--5027 Score: 384
Period size: 149 Copynumber: 1.9 Consensus size: 146
4738 AGACGGGTGT
* *
4748 CTCGGTCACCATCGGCAACCCCGACGGGTGGCTCGGCAACCCCAGGCCACGGTGCGGGAGTTCCG
1 CTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGTGCGGGAGTGCCG
* * *
4813 GACAGAGCCGAGAGTTGGTGCGGGTCCTCGGTCACCATCGGCAACCCCCGACGGTGCCTCGGCAC
66 CACAGAACCGAGAGTTGGTGCGGGTCCTCGGTCACCATCGGCAACCCCAGACGGTGCCTCGG---
4878 CCCACCACGGGTGCGGGGC
128 CCCACCACGGGTGCGGGGC
4897 CTCGGTCACCATCGGCAACCCCCGAC-GGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
1 CTCGGTCACCATCGGCAA-CCCCGACGGGTGCCTCGGCAACCCCAGGCCAC-GGTGCGGGAGTGC
* * * *
4961 CGCACAGAACCGAGCGTTGGTGCGTGAG-GCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCT
64 CGCACAGAACCGAGAGTTGGTGCG-G-GTCCTCGGTCACCATCGGCAACCCCAGAC-GGT-GCCT
5025 CGG
125 CGG
5028 TCACCATTGG
Statistics
Matches: 116, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
149 41 0.35
150 40 0.34
151 24 0.21
152 4 0.03
153 7 0.06
ACGTcount: A:0.16, C:0.37, G:0.35, T:0.12
Consensus pattern (146 bp):
CTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGTGCGGGAGTGCCG
CACAGAACCGAGAGTTGGTGCGGGTCCTCGGTCACCATCGGCAACCCCAGACGGTGCCTCGGCCC
ACCACGGGTGCGGGGC
Found at i:5064 original size:32 final size:32
Alignment explanation
Indices: 4990--5123 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
4980 GTGCGTGAGG
* *
4990 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
5023 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
5055 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
* *
5087 CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
5119 CTCGG
1 CTCGG
5124 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:5200 original size:89 final size:89
Alignment explanation
Indices: 4886--5248 Score: 313
Period size: 89 Copynumber: 3.9 Consensus size: 89
4876 ACCCCACCAC
4886 GGGTGCGGGGCCTCGGTCACCATCGGCAACCCCCGAC-GGTGCCTCGGCAACCCCAGGCCACGGG
1 GGGTGCGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGG
*
4950 TGCGGGAGTGCCGCACAGAACCGAG
66 TGCGGGAGTGCCGCACAGAGCCG-G
* * * ***
4975 CGTTGGTGCGTGAGG-CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTC-ACCATTGG
1 -G--GGTGCG-G-GGCCTCGGTCACCATCGGCAACCCCCGACGGGT-GCCTCGG-CAACCCCAGG
* * *** * ***
5038 CAAAGCCAGACGGGTGT-CTCGGTCACCATCG-GCAAA
59 CCACGGGTG-CGGGAGTGC-C-G-CA-CA--GAGCCGG
**** *
5074 CCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACG
1 GGGTG-CGGG-GCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACG
5139 GGTGCGGGAGTGCCGCACAGAGCCGG
64 GGTGCGGGAGTGCCGCACAGAGCCGG
* * **
5165 GGGTGCGGGGCCTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGTCCATTGG
1 GGGTGCGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGG
5230 TGCGGGAGTGCCGCACAGA
66 TGCGGGAGTGCCGCACAGA
5249 ACCGAGCGCT
Statistics
Matches: 209, Mismatches: 44, Indels: 41
0.71 0.15 0.14
Matches are distributed among these distances:
89 70 0.33
90 6 0.03
91 3 0.01
92 8 0.04
93 26 0.12
94 6 0.03
95 26 0.12
96 28 0.13
97 30 0.14
98 2 0.01
99 2 0.01
100 1 0.00
101 1 0.00
ACGTcount: A:0.17, C:0.35, G:0.35, T:0.13
Consensus pattern (89 bp):
GGGTGCGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGG
TGCGGGAGTGCCGCACAGAGCCGG
Found at i:18908 original size:30 final size:29
Alignment explanation
Indices: 18872--18956 Score: 98
Period size: 32 Copynumber: 2.8 Consensus size: 29
18862 TGCGTGAGCC
*
18872 CGGTCACCATCGGCAATCCCAGGGTGGCCT
1 CGGTCACCATCGGCAAACCCAGGGT-GCCT
* *
18902 CGGTCACCATCGGCAAAACCATACGGGTGTCT
1 CGGTCACCATCGGC-AAACC-CA-GGGTGCCT
*
18934 CGGTCACCATCGGCAACCCCAGG
1 CGGTCACCATCGGCAAACCCAGG
18957 CCATTGGTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
29 2 0.04
30 15 0.32
31 8 0.17
32 18 0.38
33 4 0.09
ACGTcount: A:0.21, C:0.36, G:0.27, T:0.15
Consensus pattern (29 bp):
CGGTCACCATCGGCAAACCCAGGGTGCCT
Found at i:19045 original size:32 final size:32
Alignment explanation
Indices: 19004--19117 Score: 194
Period size: 32 Copynumber: 3.6 Consensus size: 32
18994 GTGCGTGAGG
* *
19004 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
19036 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
19068 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
19100 CTCGGTCACCATCGGCAA
1 CTCGGTCACCATCGGCAA
19118 CCCCGGGTGG
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
32 67 0.85
33 12 0.15
ACGTcount: A:0.20, C:0.36, G:0.29, T:0.15
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:19414 original size:32 final size:32
Alignment explanation
Indices: 19340--19473 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
19330 GTGCGTGAGG
* *
19340 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
19373 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
19405 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
* *
19437 CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
19469 CTCGG
1 CTCGG
19474 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:27791 original size:33 final size:31
Alignment explanation
Indices: 27751--27836 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 31
27741 TGCGTGAGCC
27751 CGGTCACCATCGGCAATCCCAGGCGGGTGGCCT
1 CGGTCACCATCGGCAA-CCCAGGCGGGT-GCCT
** ** *
27784 CGGTCACCATCGGCAAAACA-TAGGGTGTCT
1 CGGTCACCATCGGCAACCCAGGCGGGTGCCT
27814 CGGTCACCATCGGCAACCCAGGC
1 CGGTCACCATCGGCAACCCAGGC
27837 CATTGGTGAG
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
30 21 0.49
31 4 0.09
32 2 0.05
33 16 0.37
ACGTcount: A:0.21, C:0.35, G:0.29, T:0.15
Consensus pattern (31 bp):
CGGTCACCATCGGCAACCCAGGCGGGTGCCT
Found at i:27924 original size:32 final size:32
Alignment explanation
Indices: 27883--28015 Score: 205
Period size: 32 Copynumber: 4.2 Consensus size: 32
27873 GTGCGTGAGG
* *
27883 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
27915 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
27947 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* * *
27979 CTCGGTCACCATCGGCAACCCCCGACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
28011 CTCGG
1 CTCGG
28016 CAACCCCAGG
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
32 83 0.87
33 12 0.13
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.14
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:28141 original size:63 final size:62
Alignment explanation
Indices: 28060--28193 Score: 234
Period size: 63 Copynumber: 2.1 Consensus size: 62
28050 AGCGAGAGTT
*
28060 GGGTGCGGGGTCCTCGGTCACCATCGGCAACCCCCGA-GGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAA-CCCAGGCCAC
28122 GGGTTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCAGGCCAC
1 GGG-TGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCAGGCCAC
28185 GGGTGCGGG
1 GGGTGCGGG
28194 AGTGCCGCAC
Statistics
Matches: 69, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
62 9 0.13
63 46 0.67
64 14 0.20
ACGTcount: A:0.13, C:0.38, G:0.37, T:0.11
Consensus pattern (62 bp):
GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCAGGCCAC
Found at i:28169 original size:32 final size:32
Alignment explanation
Indices: 28067--28171 Score: 85
Period size: 32 Copynumber: 3.3 Consensus size: 32
28057 GTTGGGTGCG
28067 GGGT-CCTCGGTCACCATCGGCAACCCCCGA-
1 GGGTGCCTCGGTCACCATCGGCAACCCCCGAC
* * ****
28097 GGGTGCCTCGG-CAACC-CCAGGCCACGGGTTG-C
1 GGGTGCCTCGGTC-ACCATC-GGCAAC-CCCCGAC
*
28129 GGGGGCCTCGGTCACCATCGGCAACCCCCGAC
1 GGGTGCCTCGGTCACCATCGGCAACCCCCGAC
28161 GGGTGCCTCGG
1 GGGTGCCTCGG
28172 CAACCCAGGC
Statistics
Matches: 53, Mismatches: 14, Indels: 14
0.65 0.17 0.17
Matches are distributed among these distances:
30 6 0.11
31 15 0.28
32 30 0.57
33 2 0.04
ACGTcount: A:0.13, C:0.40, G:0.34, T:0.12
Consensus pattern (32 bp):
GGGTGCCTCGGTCACCATCGGCAACCCCCGAC
Found at i:28302 original size:32 final size:32
Alignment explanation
Indices: 28228--28360 Score: 189
Period size: 33 Copynumber: 4.2 Consensus size: 32
28218 GTGCGTGAGG
*
28228 CTCGGTCACCATCGGCAAACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
28261 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
28293 CTCGGTCACCATCGGCAAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGC-AAACCCAGACGGGTGC
28326 CTCGGTCACCATCGGC-AACCC-GACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
28356 CTCGG
1 CTCGG
28361 CAACCCCGCC
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
30 13 0.14
31 5 0.05
32 16 0.17
33 58 0.63
ACGTcount: A:0.20, C:0.35, G:0.31, T:0.15
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:28308 original size:65 final size:63
Alignment explanation
Indices: 28228--28360 Score: 187
Period size: 65 Copynumber: 2.1 Consensus size: 63
28218 GTGCGTGAGG
* *
28228 CTCGGTCACCATCGGC-AAACCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTG
1 CTCGGTCACCATCGGCAAAACCCAGACGGGT-GCCTCGGTCACCATCGGC-AA-CCAGACGGGTG
*
28292 T
63 C
* *
28293 CTCGGTCACCATCGGCAAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCGACGGGTGC
1 CTCGGTCACCATCGGCAAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCAGACGGGTGC
28356 CTCGG
1 CTCGG
28361 CAACCCCGCC
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
63 15 0.24
64 2 0.03
65 32 0.52
66 13 0.21
ACGTcount: A:0.20, C:0.35, G:0.31, T:0.15
Consensus pattern (63 bp):
CTCGGTCACCATCGGCAAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCAGACGGGTGC
Found at i:28454 original size:345 final size:343
Alignment explanation
Indices: 27823--28461 Score: 1104
Period size: 345 Copynumber: 1.9 Consensus size: 343
27813 TCGGTCACCA
**
27823 TCGGCAACCCAGGCCATTGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGG
1 TCGGCAACCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGG
27888 TCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGT
66 TCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGT
*
27953 CACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGGCTCGGCA
131 CACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAA-CCCCGACGGGTGCCTCGGCA
* * *
28018 ACCCCAGGCCACGGGTGCGGGAGTTCGGACAGAGCGAGAGTTGGGTGCGGGGTCCTCGGTCACCA
195 ACCCCA-GCCACGGGTGCGGGAGTCCGCACAGAGCGAGAGTTGGGTGCGGGGGCCTCGGTCACCA
*
28083 TCGGCAACCCCCGAGGGTGCCTCGGCAACCCCAGGCCACGGGTTGCGGGGGCCTCGGTCACCATC
259 TCGGCAACCACCGAGGGTGCCTCGGCAACCCCAGGCCACGGGTTGCGGGGGCCTCGGTCACCATC
28148 GGCAACCCCCGACGGGTGCC
324 GGCAACCCCCGACGGGTGCC
*
28168 TCGGCAACCCAGGCCACGGGTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGG
1 TCGGCAACCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGG
* *
28233 TCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGTCTCGG
66 TCACCATCGGC-AACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
28298 TCACCATCGGCAAAACCCAGACGGGTGTCTCGGTCACCATCGGCAA-CCCGACGGGTGCCTCGGC
130 TCACCATCGGC-AAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGC
28362 AACCCC-GCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCAC
194 AACCCCAGCCACGGGTGCGGGAGT-CCGCACAGAG-CGAGAGTTGGGTGCGGGGGCCTCGGTCAC
28426 CATCGGCAA-CACCGACGGGTGCCTCGGCAACCCCAG
257 CATCGGCAACCACCGA-GGGTGCCTCGGCAACCCCAG
28462 TCCATTGGTG
Statistics
Matches: 279, Mismatches: 10, Indels: 10
0.93 0.03 0.03
Matches are distributed among these distances:
343 17 0.06
344 13 0.05
345 153 0.55
346 62 0.22
347 34 0.12
ACGTcount: A:0.18, C:0.34, G:0.35, T:0.13
Consensus pattern (343 bp):
TCGGCAACCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGG
TCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGT
CACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAA
CCCCAGCCACGGGTGCGGGAGTCCGCACAGAGCGAGAGTTGGGTGCGGGGGCCTCGGTCACCATC
GGCAACCACCGAGGGTGCCTCGGCAACCCCAGGCCACGGGTTGCGGGGGCCTCGGTCACCATCGG
CAACCCCCGACGGGTGCC
Found at i:28499 original size:91 final size:90
Alignment explanation
Indices: 28326--28503 Score: 270
Period size: 91 Copynumber: 2.0 Consensus size: 90
28316 AGACGGGTGT
28326 CTCGGTCACCATCGGCAACCCGACGGGTGCCTCGGCAACCCCGCCACGGGTGCGGGAGTGCCGCA
1 CTCGGTCACCATCGGCAACCCGACGGGTGCCTCGGCAACCCCGCCACGGGTGCGGGAGTGCCGCA
* *
28391 CAGAGCCGAGAGTTGGGTGCGGGGGC
66 CAGAACC-AGAGCTGGGTGCGGGGGC
**
28417 CTCGGTCACCATCGGCAACACCGACGGGTGCCTCGGCAACCCCAGTCCATTGGTGCGGGAGTGCC
1 CTCGGTCACCATCGGCAAC-CCGACGGGTGCCTCGGCAACCCC-G-CCACGGGTGCGGGAGTGCC
28482 GCACAGAACC-G-GCTGGGTGCGG
63 GCACAGAACCAGAGCTGGGTGCGG
28504 CAGCTCGCAC
Statistics
Matches: 80, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
91 29 0.36
92 24 0.30
93 1 0.01
94 26 0.32
ACGTcount: A:0.16, C:0.34, G:0.37, T:0.12
Consensus pattern (90 bp):
CTCGGTCACCATCGGCAACCCGACGGGTGCCTCGGCAACCCCGCCACGGGTGCGGGAGTGCCGCA
CAGAACCAGAGCTGGGTGCGGGGGC
Found at i:36657 original size:33 final size:32
Alignment explanation
Indices: 36617--36704 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 32
36607 TGCGTGAGCC
*
36617 CGGTCACCATCGGCAATCCCAGGCGGGTGGCCT
1 CGGTCACCATCGGCAAACCCAGGCGGGT-GCCT
* ** *
36650 CGGTCACCATCGGCAAAACCA-TAGGGTGTCT
1 CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
*
36681 CGGTCACCATCGGCAACCCCAGGC
1 CGGTCACCATCGGCAAACCCAGGC
36705 CATTGGTGAG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
31 22 0.49
32 4 0.09
33 19 0.42
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.15
Consensus pattern (32 bp):
CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
Found at i:36812 original size:33 final size:32
Alignment explanation
Indices: 36751--36884 Score: 198
Period size: 32 Copynumber: 4.2 Consensus size: 32
36741 GTGCGTGAGG
* *
36751 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
36783 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
36815 CTCGGTCACCCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCA-CCATCGGCAAACCCAGACGGGTGT
* * *
36848 CTCGGTCACCATCGGCAACCCCCGACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
36880 CTCGG
1 CTCGG
36885 CAACCCCAGG
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
32 51 0.54
33 44 0.46
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.14
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:36854 original size:65 final size:64
Alignment explanation
Indices: 36749--36884 Score: 202
Period size: 65 Copynumber: 2.1 Consensus size: 64
36739 TGGTGCGTGA
*
36749 GGCTCGGTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GGCTCGGTCACCATCGGCAACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
* * * *
36813 GTCTCGGTCACCCATCGGCAAACCCAGACGGGT-GTCTCGGTCACCATCGGCAACCCCCGACGGG
1 GGCTCGGTCA-CCATCGGC-AACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGG
36877 T
64 T
36878 GGCTCGG
1 GGCTCGG
36885 CAACCCCAGG
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
64 9 0.14
65 43 0.67
66 12 0.19
ACGTcount: A:0.18, C:0.37, G:0.32, T:0.14
Consensus pattern (64 bp):
GGCTCGGTCACCATCGGCAACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
Found at i:37008 original size:30 final size:30
Alignment explanation
Indices: 36968--37061 Score: 79
Period size: 30 Copynumber: 3.1 Consensus size: 30
36958 CAACCCCCGA
*
36968 CGGGTGCCTCGGCAACCCAGGCCACGGGTG
1 CGGGGGCCTCGGCAACCCAGGCCACGGGTG
* ***
36998 CGGGGGCCTCGGTC-A-CCATCGGCAAC--CCC
1 CGGGGGCCTCGG-CAACCCA--GGCCACGGGTG
37027 CGGGGTGCCTCGGCAACCCAGGCCACGGGTG
1 CGGGG-GCCTCGGCAACCCAGGCCACGGGTG
37058 CGGG
1 CGGG
37062 AGTGCCGCAC
Statistics
Matches: 47, Mismatches: 9, Indels: 15
0.66 0.13 0.21
Matches are distributed among these distances:
29 14 0.30
30 20 0.43
31 13 0.28
ACGTcount: A:0.13, C:0.38, G:0.39, T:0.10
Consensus pattern (30 bp):
CGGGGGCCTCGGCAACCCAGGCCACGGGTG
Found at i:37008 original size:62 final size:60
Alignment explanation
Indices: 36931--37061 Score: 235
Period size: 62 Copynumber: 2.1 Consensus size: 60
36921 GCCGAGAGTT
*
36931 GGGTGCGGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCG--GGGTGCCTCGGCAACCCAGGCCAC
36993 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGGGGTGCCTCGGCAACCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGGGGTGCCTCGGCAACCCAGGCCAC
37053 GGGTGCGGG
1 GGGTGCGGG
37062 AGTGCCGCAC
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
60 33 0.49
62 35 0.51
ACGTcount: A:0.13, C:0.38, G:0.38, T:0.11
Consensus pattern (60 bp):
GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGGGGTGCCTCGGCAACCCAGGCCAC
Found at i:37186 original size:31 final size:31
Alignment explanation
Indices: 37096--37226 Score: 165
Period size: 31 Copynumber: 4.2 Consensus size: 31
37086 GTGCGTGAGG
* *
37096 CTCGGTCACCATCGGCAATCCCAG-GGGGTGGC
1 CTCGGTCACCATCGGCAA-ACCAGACGGGT-GC
* *
37128 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAA-CCAGACGGGTGC
*
37160 CTCGGTCACCATCGGCAAACCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCAGACGGGTGC
* *
37191 CTCGGTCACCATCGGCAACCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCAGACGGGTGC
37222 CTCGG
1 CTCGG
37227 CAACCCCAGG
Statistics
Matches: 89, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
31 45 0.51
32 40 0.45
33 4 0.04
ACGTcount: A:0.18, C:0.34, G:0.31, T:0.16
Consensus pattern (31 bp):
CTCGGTCACCATCGGCAAACCAGACGGGTGC
Found at i:37300 original size:94 final size:92
Alignment explanation
Indices: 36993--37356 Score: 280
Period size: 94 Copynumber: 3.9 Consensus size: 92
36983 CCCAGGCCAC
36993 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCC-CGGGGTGCCTCGGCAA-CCCAGGCCACGGG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCAC-GGGTGCCTCGGCAACCCCAGGCCACGGG
*
37056 TGCGGGAGTGCCGCACAGAACCGAGCGTT
65 TGCGGGAGTGCCGCACAG-ACCGAGAGTT
* * * *** * *
37085 -GGTGCGTGAGG-CTCGGTCACCATCGGCAATCCCAGGGGGTGGCCTCGGTC-ACCATTGGCAAA
1 GGGTGCG-GGGGCCTCGGTCACCATCGGCAACCCCA-CGGGT-GCCTCGG-CAACCCCAGGCCAC
*** * * * ***
37147 GCCAGACGGGTGT-CTCGGTCAC-CATCG-GCAAAC
62 GGGTG-CGGGAGTGC-C-G-CACAGACCGAG-AGTT
** * * *
37180 CAG-ACGGGTGTCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCC-ACGGGTGCCTCGGCAACCCCAGGCCACGGG
37244 TGCGGGAGTGCCGCACAGAGCCGAGAGTT
65 TGCGGGAGTGCCGCACAGA-CCGAGAGTT
* **
37273 GGGTGCGGGGGCCTCGGTCACCATCGGCAACACCCGACGGGTG-CTCGGCAACCCCAGTCCATTG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAAC-CCC-ACGGGTGCCTCGGCAACCCCAGGCCACGG
*
37337 GTGCGGGAGTGACGCACAGA
64 GTGCGGGAGTGCCGCACAGA
37357 AACGAGCGCT
Statistics
Matches: 204, Mismatches: 47, Indels: 40
0.70 0.16 0.14
Matches are distributed among these distances:
91 30 0.15
92 9 0.04
93 20 0.10
94 91 0.45
95 48 0.24
96 3 0.01
97 3 0.01
ACGTcount: A:0.18, C:0.33, G:0.36, T:0.13
Consensus pattern (92 bp):
GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCACGGGTGCCTCGGCAACCCCAGGCCACGGGT
GCGGGAGTGCCGCACAGACCGAGAGTT
Found at i:37343 original size:342 final size:346
Alignment explanation
Indices: 36690--37326 Score: 1133
Period size: 345 Copynumber: 1.9 Consensus size: 346
36680 TCGGTCACCA
**
36690 TCGGCAACCCCAGGCCATTGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
1 TCGGCAACCCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
36755 GTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
66 GTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
*
36820 TCACCCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGGCTCGG
131 TCACCCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
* * *
36885 CAACCCCAGGCCACGGGTGCGGGAGTTCCGGACAGAGCCGAGAGTTGGGTGCGGGGTCCTCGGTC
196 CAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTC
*
36950 ACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCAGGCCACGGGTGCGGGGGCCTCGGTCACC
261 ACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCAGGCCACGGGTGCGGGGGCCTCGGTCACC
37015 ATCGGCAACCCCCGGGGTGCC
326 ATCGGCAACCCCCGGGGTGCC
*
37036 TCGGCAA-CCCAGGCCACGGGTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
1 TCGGCAACCCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
* *
37100 GTCACCATCGGCAATCCCAGG-GGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGTCTCG
66 GTCACCATCGGCAA-CCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCG
37164 GTCA-CCATCGGCAAA-CCAGACGGGTGTCTCGGTCACCATCGGCAA-CCCCGACGGGTGCCTCG
130 GTCACCCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCG
37226 GCAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGT
195 GCAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGT
37291 CACCATCGGCAACACCCGACGGGTG-CTCGGCAACCC
260 CACCATCGGCAACACCCGACGGGTGCCTCGGCAACCC
37327 CAGTCCATTG
Statistics
Matches: 280, Mismatches: 10, Indels: 7
0.94 0.03 0.02
Matches are distributed among these distances:
341 11 0.04
342 102 0.36
343 30 0.11
344 11 0.04
345 113 0.40
346 13 0.05
ACGTcount: A:0.18, C:0.34, G:0.35, T:0.13
Consensus pattern (346 bp):
TCGGCAACCCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
GTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
TCACCCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
CAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTC
ACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCAGGCCACGGGTGCGGGGGCCTCGGTCACC
ATCGGCAACCCCCGGGGTGCC
Done.