Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009488.1 Hibiscus syriacus cultivar Beakdansim tig00114591_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: 16461
ACGTcount: A:0.23, C:0.27, G:0.29, T:0.21
Found at i:4902 original size:33 final size:32
Alignment explanation
Indices: 4865--4953 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 32
4855 GCGTGAGCCC
*
4865 CGGTCACCATCGGCAATCCCAGGCGGGTGGCCT
1 CGGTCACCATCGGCAAACCCAGGCGGGT-GCCT
* ** *
4898 CGGTCACCATCGGCAAAACCATACGGGTGTCT
1 CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
*
4930 CGGTCACCATCGGCAACCCCAGGC
1 CGGTCACCATCGGCAAACCCAGGC
4954 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:5041 original size:32 final size:32
Alignment explanation
Indices: 5000--5131 Score: 205
Period size: 32 Copynumber: 4.2 Consensus size: 32
4990 GTGCGTGAGG
* *
5000 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
5032 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
5064 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* *
5096 CTCGGTCACCATCGGC-AACCCCGACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
5127 CTCGG
1 CTCGG
5132 CAACCCAGGC
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:5272 original size:60 final size:59
Alignment explanation
Indices: 5177--5305 Score: 224
Period size: 60 Copynumber: 2.2 Consensus size: 59
5167 GCCGAGAGTT
5177 GGGTGCGGGGTCCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGC-GGGTCCTCGGTCACCATCGGCAACCCCGACGGGTG-C-CGGCAACCCCAGGCCAC
5239 GGGTGCGGG-CCTCGGTCACCATCGGCAACCCCGACGGGTGCCGGCAACCCCAGGCCAC
1 GGGTGCGGGTCCTCGGTCACCATCGGCAACCCCGACGGGTGCCGGCAACCCCAGGCCAC
5297 GGGTGCGGG
1 GGGTGCGGG
5306 AGTGCCGCAC
Statistics
Matches: 67, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
58 26 0.39
59 1 0.01
60 31 0.46
61 3 0.04
62 6 0.09
ACGTcount: A:0.14, C:0.39, G:0.37, T:0.10
Consensus pattern (59 bp):
GGGTGCGGGTCCTCGGTCACCATCGGCAACCCCGACGGGTGCCGGCAACCCCAGGCCAC
Found at i:5276 original size:29 final size:29
Alignment explanation
Indices: 5188--5276 Score: 67
Period size: 29 Copynumber: 3.0 Consensus size: 29
5178 GGTGCGGGGT
5188 CCTCGGTCACCATCGGCAACCCCGACGGGTG
1 CCTCGGTCACCATCGGCAACCCCGAC-GG-G
* * ** *
5219 CCTCGG-CAACC-CCAGGCCA-CGGGTGCGGG
1 CCTCGGTC-ACCATC-GGCAACCCCG-ACGGG
5248 CCTCGGTCACCATCGGCAACCCCGACGGG
1 CCTCGGTCACCATCGGCAACCCCGACGGG
5277 TGCCGGCAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
29 18 0.43
30 10 0.24
31 14 0.33
ACGTcount: A:0.16, C:0.43, G:0.31, T:0.10
Consensus pattern (29 bp):
CCTCGGTCACCATCGGCAACCCCGACGGG
Found at i:5318 original size:152 final size:154
Alignment explanation
Indices: 5096--5377 Score: 432
Period size: 152 Copynumber: 1.8 Consensus size: 154
5086 AGACGGGTGT
*
5096 CTCGGTCACCATCGGCAACCCCGACGGGTGGCTCGGCAACCCAGGCCACGGGTGCGGGAGTTCCG
1 CTCGGTCACCATCGGCAACCCCGACGGGTGGCTCGGCAACCCAGGCCACGGGTGCGGGAGTGCCG
* * *
5161 GACAGAGCCGAGAGTTGGGTGCG-G-GGTCCTCGGTCACCATCGGCAA-CCCCGACGGGT-GCCT
66 CACAGAACCGAGAGTT-GGTGCGTGAGG--CTCGGTCACCATCGGCAATCCCAGACGGGTGGCCT
5222 CGGCAACCCCAGGCCACGGGTGCGGGC
128 CGGCAACCCCAGGCCACGGGTGCGGGC
5249 CTCGGTCACCATCGGCAACCCCGACGGGT-GC-CGGCAACCCCAGGCCACGGGTGCGGGAGTGCC
1 CTCGGTCACCATCGGCAACCCCGACGGGTGGCTCGGCAA-CCCAGGCCACGGGTGCGGGAGTGCC
* *
5312 GCACAGAACCGAGCGTTGGTGCGTGAGGCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCG
65 GCACAGAACCGAGAGTTGGTGCGTGAGGCTCGGTCACCATCGGCAATCCCAGACGGGTGGCCTCG
5377 G
130 G
5378 TCACCATTGG
Statistics
Matches: 118, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
151 30 0.25
152 50 0.42
153 38 0.32
ACGTcount: A:0.16, C:0.35, G:0.37, T:0.12
Consensus pattern (154 bp):
CTCGGTCACCATCGGCAACCCCGACGGGTGGCTCGGCAACCCAGGCCACGGGTGCGGGAGTGCCG
CACAGAACCGAGAGTTGGTGCGTGAGGCTCGGTCACCATCGGCAATCCCAGACGGGTGGCCTCGG
CAACCCCAGGCCACGGGTGCGGGC
Found at i:5414 original size:32 final size:32
Alignment explanation
Indices: 5340--5472 Score: 178
Period size: 32 Copynumber: 4.2 Consensus size: 32
5330 GTGCGTGAGG
* *
5340 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
5373 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
5405 CTCGGTCACCATCGGCAAA-CCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
* *
5436 CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
5468 CTCGG
1 CTCGG
5473 CAACCCCAGG
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
31 30 0.33
32 34 0.38
33 26 0.29
ACGTcount: A:0.18, C:0.35, G:0.31, T:0.16
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:5463 original size:63 final size:65
Alignment explanation
Indices: 5340--5472 Score: 180
Period size: 63 Copynumber: 2.1 Consensus size: 65
5330 GTGCGTGAGG
* * * * *
5340 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAATACCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGC
* * *
5405 CTCGGTCACCATCGGCAA-ACCAGACGGGT-GTCTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAATACCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGC
5468 CTCGG
1 CTCGG
5473 CAACCCCAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
63 33 0.55
64 9 0.15
65 18 0.30
ACGTcount: A:0.18, C:0.35, G:0.31, T:0.16
Consensus pattern (65 bp):
CTCGGTCACCATCGGCAATACCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:5547 original size:95 final size:95
Alignment explanation
Indices: 5436--5621 Score: 302
Period size: 95 Copynumber: 2.0 Consensus size: 95
5426 AGACGGGTGT
*
5436 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCA-CGGTGCGGGGAGTG
1 CTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCATCGGTGC-GGGAGTG
* *
5500 CCGCACAGAGCCGAGAGTTGGGTGCGGGGGC
65 CCGCACAGAACCGAGAGCTGGGTGCGGGGGC
* *
5531 CTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGTCCATTGGTGCGGGAGTGC
1 CTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCATCGGTGCGGGAGTGC
*
5596 CGCACAGAACCGAGCGCTGGGTGCGG
66 CGCACAGAACCGAGAGCTGGGTGCGG
5622 CAGCCTCGCA
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 79 0.94
96 5 0.06
ACGTcount: A:0.17, C:0.35, G:0.37, T:0.12
Consensus pattern (95 bp):
CTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCATCGGTGCGGGAGTGC
CGCACAGAACCGAGAGCTGGGTGCGGGGGC
Found at i:13840 original size:33 final size:31
Alignment explanation
Indices: 13800--13887 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 31
13790 TGCGTGAGCC
13800 CGGTCACCATCGGCAATCCCAGGCGGGTGGCCT
1 CGGTCACCATCGGCAA-CCCAGGCGGGT-GCCT
* ** *
13833 CGGTCACCATCGGCAAAACCATACGGGTGTCT
1 CGGTCACCATCGGC-AACCCAGGCGGGTGCCT
13865 CGGTCACCATCGGCAACCCAGGC
1 CGGTCACCATCGGCAACCCAGGC
13888 CATTGGTGAG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 6 0.13
32 17 0.36
33 22 0.47
34 2 0.04
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.15
Consensus pattern (31 bp):
CGGTCACCATCGGCAACCCAGGCGGGTGCCT
Found at i:13974 original size:32 final size:32
Alignment explanation
Indices: 13933--14063 Score: 205
Period size: 32 Copynumber: 4.2 Consensus size: 32
13923 GTGCGTGAGG
* *
13933 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
13965 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
13997 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
*
14029 CTCGGTCACCATCGGC-AACCC-GACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
14059 CTCGG
1 CTCGG
14064 CAACCCAGGC
Statistics
Matches: 95, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
30 13 0.14
31 5 0.05
32 65 0.68
33 12 0.13
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.15
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:14186 original size:62 final size:63
Alignment explanation
Indices: 14109--14242 Score: 252
Period size: 62 Copynumber: 2.1 Consensus size: 63
14099 GCCGAGAGTT
*
14109 GGGTGCGGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAA-CCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
14171 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
14234 GGGTGCGGG
1 GGGTGCGGG
14243 AGTGCCGCAC
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
62 51 0.73
63 19 0.27
ACGTcount: A:0.13, C:0.39, G:0.37, T:0.10
Consensus pattern (63 bp):
GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
Found at i:14207 original size:156 final size:155
Alignment explanation
Indices: 14029--14314 Score: 427
Period size: 156 Copynumber: 1.8 Consensus size: 155
14019 AGACGGGTGT
* *
14029 CTCGGTCACCATCGGCAACCCGACGGGTGGCTCGGCAA-CCCAGGCCACGGGTGCGGGAGTTCCG
1 CTCGGTCACCATCGGCAACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCG
* * *
14093 GACAGAGCCGAGAGTTGGGTGCG-G-GGTCCTCGGTCACCATCGGCAACCCCCGACGGGT-GCCT
66 CACAGAACCGAGAGTT-GGTGCGTGAGG--CTCGGTCACCATCGGCAACCCCAGACGGGTGGCCT
14155 CGGCAACCCAGGCCACGGGTGCGGGGGC
128 CGGCAACCCAGGCCACGGGTGCGGGGGC
14183 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
1 CTCGGTCACCATCGGCAA--CCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
* * *
14248 CGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTC
64 CGCACAGAACCGAGAGTTGGTGCGTGAGGCTCGGTCACCATCGGCAACCCCAGACGGGTGGCCTC
14313 GG
129 GG
14315 TCACCATTGG
Statistics
Matches: 118, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
154 18 0.15
156 52 0.44
157 46 0.39
158 2 0.02
ACGTcount: A:0.16, C:0.35, G:0.37, T:0.12
Consensus pattern (155 bp):
CTCGGTCACCATCGGCAACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCG
CACAGAACCGAGAGTTGGTGCGTGAGGCTCGGTCACCATCGGCAACCCCAGACGGGTGGCCTCGG
CAACCCAGGCCACGGGTGCGGGGGC
Found at i:14218 original size:94 final size:91
Alignment explanation
Indices: 13997--14219 Score: 218
Period size: 94 Copynumber: 2.4 Consensus size: 91
13987 AGACGGGTGT
* *
13997 CTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCGACGGGTGGCTC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCGACGGGTGCCTC
14062 GGCAACCCAGGCCACGGGTGCGGGAG
66 GGCAACCCAGGCCACGGGTGCGGGAG
* * * * * ***** *
14088 TTCCGGACA-GAGCCG-AGAGTTGGGTGCGGG-GTCCTCGGTCACCATCGGCAACCCCCGACGGG
1 CT-CGGTCACCATCGGCA-AACCCAG-ACGGGTG-CCTCGGTCACCATCGGCAA--CCCGACGGG
*
14150 TGCCTCGGCAACCCAGGCCACGGGTGCGGGGG
60 TGCCTCGGCAACCCAGGCCACGGGTGCGGGAG
* *
14182 CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
1 -CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGG
14220 CAACCCCAGG
Statistics
Matches: 97, Mismatches: 25, Indels: 17
0.70 0.18 0.12
Matches are distributed among these distances:
90 1 0.01
91 7 0.07
92 27 0.28
94 54 0.56
95 7 0.07
96 1 0.01
ACGTcount: A:0.16, C:0.36, G:0.35, T:0.13
Consensus pattern (91 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCGACGGGTGCCTC
GGCAACCCAGGCCACGGGTGCGGGAG
Found at i:14270 original size:94 final size:94
Alignment explanation
Indices: 14172--14556 Score: 343
Period size: 94 Copynumber: 4.1 Consensus size: 94
14162 CCAGGCCACG
14172 GGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGG
1 GGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGG
14237 TGCGGGAGTGCCGCACAGAACCGAGCGTT
66 TGCGGGAGTGCCGCACAGAACCGAGCGTT
* * * * *** * *
14266 GGTGCGTGAGG-CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTC-ACCATTGGCAAA
1 GGTGCG-GGGGCCTCGGTCACCATCGGCAACCCCCGACGGGT-GCCTCGG-CAACCCCAGGCCAC
*** * ** ** * ***
14329 GCCAGACGGGTGT-CTCGGTCACCATCG-GCAAAC
63 GGGTG-CGGGAGTGC-CGCACAGAACCGAGC-GTT
*** * *
14362 CCAGACGGGTGTCTCGGTCACCATCGGCAA-CCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
1 GGTG-CGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
* *
14426 GTGCGGGAGTGCCGCACAGAGCCGAGAGTT
65 GTGCGGGAGTGCCGCACAGAACCGAGCGTT
* * **
14456 GGGTGCGGGGGCCTCGGTCACCATCGGCAACACCCGACGGGTG-C-CGGCAACCCCAGTCCATTG
1 -GGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
*
14519 GTGCGGGAGTGCCGCACAGAACCGAGCGCTG
65 GTGCGGGAGTGCCGCACAGAACCGAGCG-TT
14550 GGTGCGG
1 GGTGCGG
14557 CAGCCTCGCA
Statistics
Matches: 218, Mismatches: 59, Indels: 29
0.71 0.19 0.09
Matches are distributed among these distances:
93 49 0.22
94 71 0.33
95 52 0.24
96 26 0.12
97 20 0.09
ACGTcount: A:0.17, C:0.34, G:0.36, T:0.13
Consensus pattern (94 bp):
GGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGG
TGCGGGAGTGCCGCACAGAACCGAGCGTT
Found at i:14351 original size:32 final size:32
Alignment explanation
Indices: 14277--14409 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
14267 GTGCGTGAGG
* *
14277 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
14310 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
14342 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
14374 CTCGGTCACCATCGGC-AACCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
14405 CTCGG
1 CTCGG
14410 CAACCCCAGG
Statistics
Matches: 91, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
31 18 0.20
32 47 0.52
33 26 0.29
ACGTcount: A:0.18, C:0.35, G:0.31, T:0.16
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:14357 original size:65 final size:63
Alignment explanation
Indices: 14277--14409 Score: 185
Period size: 65 Copynumber: 2.1 Consensus size: 63
14267 GTGCGTGAGG
* * * * *
14277 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GCCTCGGTCACCATCGGC-AACCCAGACGGGTGC
* *
14342 CTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCAGACGGGTGC
14405 CTCGG
1 CTCGG
14410 CAACCCCAGG
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 17 0.28
64 16 0.26
65 28 0.46
ACGTcount: A:0.18, C:0.35, G:0.31, T:0.16
Consensus pattern (63 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCAGACGGGTGC
Found at i:14506 original size:345 final size:342
Alignment explanation
Indices: 13874--14508 Score: 1121
Period size: 345 Copynumber: 1.8 Consensus size: 342
13864 TCGGTCACCA
**
13874 TCGGCAACCCAGGCCATTGGTGAGGGAGTGCCGCACAGAACGAGCGTTGGTGCGTGAGGCTCGGT
1 TCGGCAACCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACGAGCGTTGGTGCGTGAGGCTCGGT
13939 CACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTC
66 CACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTC
*
14004 ACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCGACGGGTGGCTCGGCAACC
131 ACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCGACGGGTGCCTCGGCAACC
* * *
14069 CAGGCCACGGGTGCGGGAGTTCCGGACAGAGCCGAGAGTTGGGTGCGGGGTCCTCGGTCACCATC
196 CAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCACCATC
*
14134 GGCAACCCCCGACGGGTGCCTCGGCAACCCAGGCCACGGGTGCGGGGGCCTCGGTCACCATCGGC
261 GGCAACACCCGACGGGTGCCTCGGCAACCCAGGCCACGGGTGCGGGGGCCTCGGTCACCATCGGC
14199 AACCCCCGACGGGTGCC
326 AACCCCCGACGGGTGCC
*
14216 TCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
1 TCGGCAA-CCCAGGCCACGGGTGAGGGAGTGCCGCACAGAA-CGAGCGTTGGTGCGTGAGGCTCG
* *
14281 GTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGTCTCG
64 GTCACCATCGGCAA-CCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCG
14346 GTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGC
128 GTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAA-CCCGACGGGTGCCTCGGC
14411 AACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCA
192 AA-CCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCA
14476 CCATCGGCAACACCCGACGGGTG-C-CGGCAACCC
256 CCATCGGCAACACCCGACGGGTGCCTCGGCAACCC
14509 CAGTCCATTG
Statistics
Matches: 278, Mismatches: 10, Indels: 7
0.94 0.03 0.02
Matches are distributed among these distances:
342 7 0.03
343 30 0.11
344 37 0.13
345 103 0.37
346 20 0.07
347 81 0.29
ACGTcount: A:0.18, C:0.34, G:0.35, T:0.13
Consensus pattern (342 bp):
TCGGCAACCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACGAGCGTTGGTGCGTGAGGCTCGGT
CACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTC
ACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCGACGGGTGCCTCGGCAACC
CAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCACCATC
GGCAACACCCGACGGGTGCCTCGGCAACCCAGGCCACGGGTGCGGGGGCCTCGGTCACCATCGGC
AACCCCCGACGGGTGCC
Found at i:14563 original size:93 final size:94
Alignment explanation
Indices: 14171--14564 Score: 316
Period size: 93 Copynumber: 4.2 Consensus size: 94
14161 CCCAGGCCAC
**
14171 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
1 GGGTGCGGCAGCCTCGGTCACCATCGGCAA-CCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
*
14236 GTGCGGGAGTGCCGCACAGAACCGAGCG-T
65 GTGCGGGAGTGCCGCACAGAACCGAGAGCT
* * * * *
14265 TGGTGCGTG-AGGCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTC-ACCATTGGCAA
1 GGGTGCG-GCAGCCTCGGTCACCATCGGCAA-CCCCGACGGGT-GCCTCGG-CAACC-----CCA
* ** * *
14328 AGCCAGACGGGTGTCTCG-GT-CAC-CATCGGCAAACCCAGA-C-
57 GGCC--ACGGGTG-CGGGAGTGC-CGCA-CAG--AACCGAGAGCT
*
14368 GGGT------GTCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGG
1 GGGTGCGGCAGCCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGG
* *
14427 TGCGGGAGTGCCGCACAGAGCCGAGAGTT
66 TGCGGGAGTGCCGCACAGAACCGAGAGCT
** * **
14456 GGGTGCGGGGGCCTCGGTCACCATCGGCAACACCCGACGGGTG-C-CGGCAACCCCAGTCCATTG
1 GGGTGCGGCAGCCTCGGTCACCATCGGCAAC-CCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
*
14519 GTGCGGGAGTGCCGCACAGAACCGAGCGCT
65 GTGCGGGAGTGCCGCACAGAACCGAGAGCT
14549 GGGTGCGGCAGCCTCG
1 GGGTGCGGCAGCCTCG
14565 CACAGCGTCG
Statistics
Matches: 237, Mismatches: 34, Indels: 59
0.72 0.10 0.18
Matches are distributed among these distances:
86 6 0.03
87 2 0.01
88 16 0.07
89 3 0.01
90 5 0.02
93 57 0.24
94 56 0.24
95 32 0.14
96 10 0.04
97 19 0.08
100 5 0.02
101 3 0.01
102 12 0.05
103 5 0.02
104 6 0.03
ACGTcount: A:0.17, C:0.34, G:0.36, T:0.13
Consensus pattern (94 bp):
GGGTGCGGCAGCCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGG
TGCGGGAGTGCCGCACAGAACCGAGAGCT
Done.