Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009530.1 Hibiscus syriacus cultivar Beakdansim tig00116170_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: 33556
ACGTcount: A:0.22, C:0.27, G:0.28, T:0.23
Found at i:7551 original size:33 final size:32
Alignment explanation
Indices: 7514--7602 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 32
7504 GCGTGAGCCC
*
7514 CGGTCACCATCGGCAATCCCAGGCGGGTGGCCT
1 CGGTCACCATCGGCAAACCCAGGCGGGT-GCCT
* ** *
7547 CGGTCACCATCGGCAAAACCATACGGGTGTCT
1 CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
*
7579 CGGTCACCATCGGCAACCCCAGGC
1 CGGTCACCATCGGCAAACCCAGGC
7603 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:7690 original size:32 final size:32
Alignment explanation
Indices: 7649--7781 Score: 205
Period size: 32 Copynumber: 4.2 Consensus size: 32
7639 GTGCGTGAGG
* *
7649 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
7681 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
7713 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* * *
7745 CTCGGTCACCATCGGCAACCCCCGACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
7777 CTCGG
1 CTCGG
7782 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:7906 original size:31 final size:31
Alignment explanation
Indices: 7865--7962 Score: 92
Period size: 31 Copynumber: 3.1 Consensus size: 31
7855 CAACCCCCGA
7865 CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
1 CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
* * * ****
7896 CGGGGGCCTCGGTC-ACCATC-GGCAACCCCCG
1 CGGGTGCCTCGG-CAACC-CCAGGCCACGGGTG
7927 ACGGGTGCCTCGGCAACCCCAGGCCACGGGTG
1 -CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
7959 CGGG
1 CGGG
7963 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:7927 original size:63 final size:63
Alignment explanation
Indices: 7828--7962 Score: 261
Period size: 63 Copynumber: 2.1 Consensus size: 63
7818 GCCGAGAGTT
*
7828 GGGTGCGGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
7891 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
7954 GGGTGCGGG
1 GGGTGCGGG
7963 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:7938 original size:95 final size:94
Alignment explanation
Indices: 7713--7939 Score: 244
Period size: 95 Copynumber: 2.4 Consensus size: 94
7703 AGACGGGTGT
* *
7713 CTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCC
7778 TCGGCAACCCCAGGCCACGGGTGCGGGAG
66 TCGGCAACCCCAGGCCACGGGTGCGGGAG
* * * * * ***** *
7807 TTCCGGACA-GAGCCG-AGAGTTGGGTGCGGG-GTCCTCGGTCACCATCGGCAACCCCCGACGGG
1 CT-CGGTCACCATCGGCA-AACCCAG-ACGGGTG-CCTCGGTCACCATCGGCAACCCCCGACGGG
*
7869 TGCCTCGGCAACCCCAGGCCACGGGTGCGGGGG
62 TGCCTCGGCAACCCCAGGCCACGGGTGCGGGAG
* *
7902 CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
1 -CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGG
7940 CAACCCCAGG
Statistics
Matches: 100, Mismatches: 25, Indels: 15
0.71 0.18 0.11
Matches are distributed among these distances:
93 1 0.01
94 7 0.07
95 84 0.84
96 7 0.07
97 1 0.01
ACGTcount: A:0.16, C:0.37, G:0.35, T:0.12
Consensus pattern (94 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCC
TCGGCAACCCCAGGCCACGGGTGCGGGAG
Found at i:7939 original size:158 final size:158
Alignment explanation
Indices: 7745--8034 Score: 460
Period size: 158 Copynumber: 1.8 Consensus size: 158
7735 AGACGGGTGT
* *
7745 CTCGGTCACCATCGGCAACCCCCGACGGGTGGCTCGGCAACCCCAGGCCACGGGTGCGGGAGTTC
1 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
* * *
7810 CGGACAGAGCCGAGAGTTGGGTGCG-G-GGTCCTCGGTCACCATCGGCAACCCCCGACGGGT-GC
66 CGCACAGAACCGAGAGTT-GGTGCGTGAGG--CTCGGTCACCATCGGCAACCCCAGACGGGTGGC
7872 CTCGGCAACCCCAGGCCACGGGTGCGGGGGC
128 CTCGGCAACCCCAGGCCACGGGTGCGGGGGC
7903 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
1 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
* * *
7968 CGCACAGAACCGAGCGTTGGTGCGTGAGGCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTC
66 CGCACAGAACCGAGAGTTGGTGCGTGAGGCTCGGTCACCATCGGCAACCCCAGACGGGTGGCCTC
8033 GG
131 GG
8035 TCACCATTGG
Statistics
Matches: 121, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
157 33 0.27
158 86 0.71
159 2 0.02
ACGTcount: A:0.16, C:0.36, G:0.37, T:0.12
Consensus pattern (158 bp):
CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
CGCACAGAACCGAGAGTTGGTGCGTGAGGCTCGGTCACCATCGGCAACCCCAGACGGGTGGCCTC
GGCAACCCCAGGCCACGGGTGCGGGGGC
Found at i:8071 original size:32 final size:32
Alignment explanation
Indices: 7997--8130 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
7987 GTGCGTGAGG
* *
7997 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
8030 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
8062 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
* *
8094 CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
8126 CTCGG
1 CTCGG
8131 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:8213 original size:95 final size:95
Alignment explanation
Indices: 7891--8279 Score: 369
Period size: 95 Copynumber: 4.1 Consensus size: 95
7881 CCCAGGCCAC
7891 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
*
7956 GTGCGGGAGTGCCGCACAGAACCGAGCG-T
66 GTGCGGGAGTGCCGCACAGAACCGAGAGCT
* * * * * *** *
7985 TGGTGCGTGAGG-CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTC-ACCATTGGCAA
1 GGGTGCG-GGGGCCTCGGTCACCATCGGCAACCCCCGACGGGT-GCCTCGG-CAACCCCAGGCCA
* *** * * * * * *
8048 AGCCAGACGGGTGT-CTCGGTCAC-CATCGGCA-AACC
63 CGGGTG-CGGGAGTGC-C-G-CACAGAACCG-AGAGCT
** * * *
8083 CAG-ACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
* *
8147 GTGCGGGAGTGCCGCACAGAGCCGAGAGTT
66 GTGCGGGAGTGCCGCACAGAACCGAGAGCT
* * **
8177 GGGTGCGGGGGCCTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGTCCATTG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
*
8242 GTGCGGGAGTGCCGCACAGAACCGAGCGCT
66 GTGCGGGAGTGCCGCACAGAACCGAGAGCT
8272 GGGTGCGG
1 GGGTGCGG
8280 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:8226 original size:349 final size:348
Alignment explanation
Indices: 7588--8248 Score: 1196
Period size: 349 Copynumber: 1.9 Consensus size: 348
7578 TCGGTCACCA
**
7588 TCGGCAACCCCAGGCCATTGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
1 TCGGCAACCCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
7653 GTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
66 GTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
*
7718 TCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGGCTCGGC
131 TCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGC
* * *
7783 AACCCCAGGCCACGGGTGCGGGAGTTCCGGACAGAGCCGAGAGTTGGGTGCGGGGTCCTCGGTCA
196 AACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCA
*
7848 CCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACC
261 CCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACC
7913 ATCGGCAACCCCCGACGGGTGCC
326 ATCGGCAACCCCCGACGGGTGCC
*
7936 TCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
1 TCGGCAACCCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
* *
8001 GTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGTCTCG
66 GTCACCATCGGCAA-CCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCG
8066 GTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
130 GTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
8131 CAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTC
195 CAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTC
* **
8196 ACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGTCCATTGGTGCGGG
260 ACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGG
8249 AGTGCCGCAC
Statistics
Matches: 299, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
348 76 0.25
349 223 0.75
ACGTcount: A:0.17, C:0.34, G:0.35, T:0.13
Consensus pattern (348 bp):
TCGGCAACCCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
GTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
TCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGC
AACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCA
CCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACC
ATCGGCAACCCCCGACGGGTGCC
Found at i:22219 original size:32 final size:33
Alignment explanation
Indices: 22143--22227 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
22133 GTGTGCGTGC
* * *
22143 GCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
22176 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
22208 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
22228 CCCCGACCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 19 0.40
33 28 0.60
ACGTcount: A:0.20, C:0.34, G:0.29, T:0.16
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
Found at i:22350 original size:31 final size:32
Alignment explanation
Indices: 22312--22394 Score: 123
Period size: 31 Copynumber: 2.6 Consensus size: 32
22302 GTGTGCGTGA
* *
22312 GCCTCGGTCACCATCGGCAATCCAAGGCGGG-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGT
*
22343 GCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGT
*
22375 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
22395 CCCCGGGCCA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 28 0.60
32 19 0.40
ACGTcount: A:0.20, C:0.36, G:0.29, T:0.14
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAAACCAAGACGGGT
Found at i:22515 original size:167 final size:170
Alignment explanation
Indices: 22006--22583 Score: 1015
Period size: 167 Copynumber: 3.4 Consensus size: 170
21996 ACGTGTGCGT
**
22006 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
22071 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* *
22136 TGCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
22176 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GACCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
22240 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
22305 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGC-GG-G
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
22343 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
22408 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG-CCGC-T-
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
*
22470 TGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
22510 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
22575 GTGCGGGAG
66 GTGCGGGAG
22584 CCTCGGTCAC
Statistics
Matches: 391, Mismatches: 14, Indels: 9
0.94 0.03 0.02
Matches are distributed among these distances:
165 34 0.09
166 3 0.01
167 134 0.34
168 63 0.16
169 103 0.26
170 54 0.14
ACGTcount: A:0.17, C:0.34, G:0.33, T:0.16
Consensus pattern (170 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:22519 original size:33 final size:33
Alignment explanation
Indices: 22477--22667 Score: 197
Period size: 33 Copynumber: 5.6 Consensus size: 33
22467 GCTTGCGTGA
*
22477 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
22510 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
* * * * *
22542 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG
**
22582 AGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
22616 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
22648 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
22668 CCCCGGGCCA
Statistics
Matches: 131, Mismatches: 18, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
32 41 0.31
33 60 0.46
34 2 0.02
35 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 1 0.01
41 22 0.17
ACGTcount: A:0.17, C:0.36, G:0.31, T:0.16
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
Found at i:22556 original size:65 final size:66
Alignment explanation
Indices: 22477--22667 Score: 197
Period size: 65 Copynumber: 2.8 Consensus size: 66
22467 GCTTGCGTGA
*
22477 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
22542 -
66 G
* * * * * **
22542 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGGAGCCTCGGTCACCATCGGCAGTCCC
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG-GCCTCGGTCACCATCGGCAAACCC
*
22607 AGGCGGGTG
58 AGACGGGTG
* *
22616 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAA
22668 CCCCGGGCCA
Statistics
Matches: 101, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
65 41 0.41
66 1 0.01
67 1 0.01
68 1 0.01
69 1 0.01
70 1 0.01
71 1 0.01
72 2 0.02
73 30 0.30
74 22 0.22
ACGTcount: A:0.17, C:0.36, G:0.31, T:0.16
Consensus pattern (66 bp):
GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
G
Found at i:22660 original size:106 final size:106
Alignment explanation
Indices: 22470--22686 Score: 407
Period size: 106 Copynumber: 2.0 Consensus size: 106
22460 TCAGGCCGCT
*
22470 TGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCA
1 TGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCA
*
22535 GACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTGG
66 GACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGG
*
22576 TGCGGGAGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCA
1 TGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCA
22641 GACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGG
66 GACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGG
22682 TGCGG
1 TGCGG
22687 AGTGCCGCAC
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 108 1.00
ACGTcount: A:0.16, C:0.35, G:0.33, T:0.16
Consensus pattern (106 bp):
TGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCA
GACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGG
Found at i:23072 original size:11 final size:11
Alignment explanation
Indices: 23058--23089 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
23048 TCCCGGTGGT
23058 GCTCCGGCGAC
1 GCTCCGGCGAC
*
23069 GCTCCGGCGAT
1 GCTCCGGCGAC
23080 GCTCCGGCGA
1 GCTCCGGCGA
23090 GACATTATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.38, T:0.12
Consensus pattern (11 bp):
GCTCCGGCGAC
Found at i:31227 original size:32 final size:33
Alignment explanation
Indices: 31151--31235 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
31141 GTGTGCGTGC
* * *
31151 GCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
31184 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
31216 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
31236 CCCCGACCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 19 0.40
33 28 0.60
ACGTcount: A:0.20, C:0.34, G:0.29, T:0.16
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
Found at i:31312 original size:169 final size:169
Alignment explanation
Indices: 31015--31592 Score: 1011
Period size: 169 Copynumber: 3.4 Consensus size: 169
31005 ACGTGTGCGT
**
31015 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
31080 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
* *
31145 GCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
131 GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
31184 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GACCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
31248 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGG-CCCCGTG
31313 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
130 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
31353 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATT-
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* * *
31417 -TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGGCCGCTTGT
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
*
31481 GCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
131 GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
31520 GCCTCGGTCACCATCGGCAAACCCAGAC-GGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
31584 GTGCGGGAG
66 GTGCGGGAG
31593 CCTCGGTCAC
Statistics
Matches: 390, Mismatches: 15, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
166 34 0.09
167 72 0.18
168 123 0.32
169 155 0.40
170 6 0.02
ACGTcount: A:0.17, C:0.34, G:0.33, T:0.16
Consensus pattern (169 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:31396 original size:32 final size:33
Alignment explanation
Indices: 31320--31404 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
31310 GTGTGCGTGA
* *
31320 GCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
31353 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
31385 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
31405 CCCCGGGCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
32 19 0.40
33 29 0.60
ACGTcount: A:0.20, C:0.35, G:0.29, T:0.15
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
Found at i:31560 original size:64 final size:65
Alignment explanation
Indices: 31487--31675 Score: 193
Period size: 64 Copynumber: 2.8 Consensus size: 65
31477 TTGTGCGTGA
*
31487 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGTG
* * * * * **
31551 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGGAGCCTCGGTCACCATCGGCAGTCCC
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG-GCCTCGGTCACCATCGGCAAACCC
*
31616 AGGCGGTG
58 AGACGGTG
* *
31624 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAA
31676 CCCCGGGCCA
Statistics
Matches: 100, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
64 41 0.41
65 1 0.01
66 1 0.01
67 1 0.01
68 1 0.01
69 1 0.01
70 1 0.01
71 2 0.02
72 29 0.29
73 22 0.22
ACGTcount: A:0.17, C:0.36, G:0.31, T:0.16
Consensus pattern (65 bp):
GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGTG
Found at i:31602 original size:105 final size:105
Alignment explanation
Indices: 31479--31697 Score: 395
Period size: 105 Copynumber: 2.1 Consensus size: 105
31469 CAGGCCGCTT
*
31479 GTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGC-GGTGGCCTCGGTCACCATCGGCAAACCC
*
31544 AGAC-GGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
65 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
*
31584 GTGCGGGAGCCTCGGTCACCATCGGCAGTCCCAGGCGGTGGCCTCGGTCACCATCGGCAAACCCA
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGTGGCCTCGGTCACCATCGGCAAACCCA
31649 GACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
66 GACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
31689 GTGCGGGAG
1 GTGCGGGAG
31698 TGCCGCACAG
Statistics
Matches: 110, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
104 32 0.29
105 78 0.71
ACGTcount: A:0.16, C:0.35, G:0.33, T:0.16
Consensus pattern (105 bp):
GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGTGGCCTCGGTCACCATCGGCAAACCCA
GACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
Found at i:31628 original size:32 final size:32
Alignment explanation
Indices: 31587--31675 Score: 117
Period size: 32 Copynumber: 2.8 Consensus size: 32
31577 GCCATTGGTG
* ** *
31587 CGGGAGCCTCGGTCACCATCGGCAGTCCCAGG
1 CGGGTGCCTCGGTCACCATCGGCAAACCCAGA
31619 C-GGTGGCCTCGGTCACCATCGGCAAACCCAGA
1 CGGGT-GCCTCGGTCACCATCGGCAAACCCAGA
*
31651 CGGGTGTCTCGGTCACCATCGGCAA
1 CGGGTGCCTCGGTCACCATCGGCAA
31676 CCCCGGGCCA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
31 2 0.04
32 45 0.90
33 3 0.06
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.15
Consensus pattern (32 bp):
CGGGTGCCTCGGTCACCATCGGCAAACCCAGA
Found at i:31734 original size:104 final size:103
Alignment explanation
Indices: 31520--31827 Score: 329
Period size: 105 Copynumber: 3.1 Consensus size: 103
31510 CAGGCGGGTG
*
31520 GCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGG
* ** ** * *
31585 TGCGGGAG-CCTCGGTCACCATC-GGCAGTCCCAG-GCGGTG-
66 TGCGGGAGTAC-CGCACAGAACCGGGC-GT--CGGTGCGG-GA
31624 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGAC-GGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
31689 GTGCGGGAGTGCCGCACAGAACCGGGCGTTGGTGCGGGA
65 GTGCGGGAGTACCGCACAGAACCGGGCGTCGGTGCGGGA
* *
31728 GCCTCGGTCACCATCGGC-AACCCCGACGG-G--T--G---CC-TCGGCAACCCCAGGCCATTGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGG
* *
31783 TGCGGGAGTACCGCACAGAACCGAGCGCTGGGTGCGGGA
66 TGCGGGAGTACCGCACAGAACCGGGCG-TCGGTGCGGGA
31822 GCCTCG
1 GCCTCG
31828 CACAGCGTCG
Statistics
Matches: 184, Mismatches: 14, Indels: 22
0.84 0.06 0.10
Matches are distributed among these distances:
93 45 0.24
94 18 0.10
97 1 0.01
99 1 0.01
101 1 0.01
102 2 0.01
103 10 0.05
104 50 0.27
105 52 0.28
106 4 0.02
ACGTcount: A:0.17, C:0.35, G:0.34, T:0.14
Consensus pattern (103 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGG
TGCGGGAGTACCGCACAGAACCGGGCGTCGGTGCGGGA
Found at i:32079 original size:11 final size:11
Alignment explanation
Indices: 32065--32096 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
32055 TCCCGGTGGT
32065 GCTCCGGCGAC
1 GCTCCGGCGAC
*
32076 GCTCCGGCGAT
1 GCTCCGGCGAC
32087 GCTCCGGCGA
1 GCTCCGGCGA
32097 GACATTATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.38, T:0.12
Consensus pattern (11 bp):
GCTCCGGCGAC
Done.