Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009464.1 Hibiscus syriacus cultivar Beakdansim tig00113803_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: 50053
ACGTcount: A:0.22, C:0.27, G:0.28, T:0.23
Found at i:5564 original size:32 final size:33
Alignment explanation
Indices: 5488--5572 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
5478 GTGTGCGTGC
* * *
5488 GCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
5521 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
5553 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
5573 CCCCGGCCAT
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:5631 original size:169 final size:170
Alignment explanation
Indices: 5352--5932 Score: 1042
Period size: 169 Copynumber: 3.4 Consensus size: 170
5342 ACGTGTGCGT
**
5352 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAA-CCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
5416 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* *
5481 TGCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
5521 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
5585 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
5650 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
5690 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* * *
5755 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG-CCGCTTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
*
5819 TGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
5859 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
5924 GTGCGGGAG
66 GTGCGGGAG
5933 CCTCGGTCAC
Statistics
Matches: 397, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
169 332 0.84
170 65 0.16
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.16
Consensus pattern (170 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:5733 original size:32 final size:33
Alignment explanation
Indices: 5657--5741 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
5647 GTGTGCGTGA
* *
5657 GCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
5690 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
5722 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
5742 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:5868 original size:33 final size:33
Alignment explanation
Indices: 5826--6016 Score: 197
Period size: 33 Copynumber: 5.6 Consensus size: 33
5816 TTGTGCGTGA
*
5826 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
5859 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
* * * * *
5891 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG
**
5931 AGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
5965 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
5997 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
6017 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:5900 original size:65 final size:66
Alignment explanation
Indices: 5826--6016 Score: 197
Period size: 65 Copynumber: 2.8 Consensus size: 66
5816 TTGTGCGTGA
*
5826 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
5891 -
66 G
* * * * * **
5891 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGGAGCCTCGGTCACCATCGGCAGTCCC
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG-GCCTCGGTCACCATCGGCAAACCC
*
5956 AGGCGGGTG
58 AGACGGGTG
* *
5965 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAA
6017 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:5943 original size:106 final size:106
Alignment explanation
Indices: 5818--6038 Score: 415
Period size: 106 Copynumber: 2.1 Consensus size: 106
5808 CAGGCCGCTT
*
5818 GTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
*
5883 AGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
*
5924 GTGCGGGAGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
5989 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
6030 GTGCGGGAG
1 GTGCGGGAG
6039 TGCCGCACAG
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 112 1.00
ACGTcount: A:0.16, C:0.34, G:0.33, T:0.16
Consensus pattern (106 bp):
GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
Found at i:6420 original size:11 final size:11
Alignment explanation
Indices: 6406--6437 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
6396 TCCCGGTGGT
6406 GCTCCGGCGAC
1 GCTCCGGCGAC
*
6417 GCTCCGGCGAT
1 GCTCCGGCGAC
6428 GCTCCGGCGA
1 GCTCCGGCGA
6438 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:14576 original size:32 final size:33
Alignment explanation
Indices: 14500--14584 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
14490 GTGTGCGTGC
* * *
14500 GCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
14533 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
14565 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
14585 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:14744 original size:32 final size:33
Alignment explanation
Indices: 14668--14752 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
14658 GTGTGCGTGA
* *
14668 GCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
14701 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
14733 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
14753 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:14766 original size:169 final size:170
Alignment explanation
Indices: 14363--14943 Score: 1033
Period size: 169 Copynumber: 3.4 Consensus size: 170
14353 ACGTGTGCGT
**
14363 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
14428 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* *
14493 TGCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
14533 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GACCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
14597 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGC-GGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
14661 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
14701 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* * *
14766 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG-CCGCTTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
*
14830 TGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
14870 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
14935 GTGCGGGAG
66 GTGCGGGAG
14944 CCTCGGTCAC
Statistics
Matches: 394, Mismatches: 15, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
168 123 0.31
169 197 0.50
170 74 0.19
ACGTcount: A:0.17, C:0.34, G:0.33, T:0.16
Consensus pattern (170 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:14879 original size:33 final size:33
Alignment explanation
Indices: 14837--15027 Score: 197
Period size: 33 Copynumber: 5.6 Consensus size: 33
14827 TTGTGCGTGA
*
14837 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
14870 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
* * * * *
14902 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG
**
14942 AGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
14976 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
15008 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
15028 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:14911 original size:65 final size:66
Alignment explanation
Indices: 14837--15027 Score: 197
Period size: 65 Copynumber: 2.8 Consensus size: 66
14827 TTGTGCGTGA
*
14837 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
14902 -
66 G
* * * * * **
14902 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGGAGCCTCGGTCACCATCGGCAGTCCC
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG-GCCTCGGTCACCATCGGCAAACCC
*
14967 AGGCGGGTG
58 AGACGGGTG
* *
14976 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAA
15028 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:14954 original size:106 final size:106
Alignment explanation
Indices: 14829--15049 Score: 415
Period size: 106 Copynumber: 2.1 Consensus size: 106
14819 CAGGCCGCTT
*
14829 GTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
*
14894 AGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
*
14935 GTGCGGGAGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
15000 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
15041 GTGCGGGAG
1 GTGCGGGAG
15050 TGCCGCACAG
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 112 1.00
ACGTcount: A:0.16, C:0.34, G:0.33, T:0.16
Consensus pattern (106 bp):
GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
Found at i:15433 original size:11 final size:11
Alignment explanation
Indices: 15419--15450 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
15409 TCCCGGTGGT
15419 GCTCCGGCGAC
1 GCTCCGGCGAC
*
15430 GCTCCGGCGAT
1 GCTCCGGCGAC
15441 GCTCCGGCGA
1 GCTCCGGCGA
15451 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:27968 original size:32 final size:33
Alignment explanation
Indices: 27892--27976 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
27882 GTGTGCGTGC
* * *
27892 GCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
27925 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
27957 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
27977 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:28039 original size:169 final size:170
Alignment explanation
Indices: 27755--28336 Score: 1042
Period size: 169 Copynumber: 3.4 Consensus size: 170
27745 ACGTGTGCGT
**
27755 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
27820 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* *
27885 TGCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
27925 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GACCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
27989 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
28054 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
28094 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* * *
28159 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG-CCGCTTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
*
28223 TGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
28263 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
28328 GTGCGGGAG
66 GTGCGGGAG
28337 CCTCGGTCAC
Statistics
Matches: 396, Mismatches: 15, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
169 281 0.71
170 115 0.29
ACGTcount: A:0.17, C:0.34, G:0.33, T:0.16
Consensus pattern (170 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:28137 original size:32 final size:33
Alignment explanation
Indices: 28061--28145 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
28051 GTGTGCGTGA
* *
28061 GCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
28094 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
28126 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
28146 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:28272 original size:33 final size:33
Alignment explanation
Indices: 28230--28420 Score: 197
Period size: 33 Copynumber: 5.6 Consensus size: 33
28220 TTGTGCGTGA
*
28230 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
28263 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
* * * * *
28295 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG
**
28335 AGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
28369 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
28401 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
28421 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:28304 original size:65 final size:66
Alignment explanation
Indices: 28230--28420 Score: 197
Period size: 65 Copynumber: 2.8 Consensus size: 66
28220 TTGTGCGTGA
*
28230 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
28295 -
66 G
* * * * * **
28295 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGGAGCCTCGGTCACCATCGGCAGTCCC
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG-GCCTCGGTCACCATCGGCAAACCC
*
28360 AGGCGGGTG
58 AGACGGGTG
* *
28369 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAA
28421 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:28347 original size:106 final size:106
Alignment explanation
Indices: 28222--28442 Score: 415
Period size: 106 Copynumber: 2.1 Consensus size: 106
28212 CAGGCCGCTT
*
28222 GTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
*
28287 AGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
*
28328 GTGCGGGAGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
28393 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
28434 GTGCGGGAG
1 GTGCGGGAG
28443 TGCCGCACAG
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 112 1.00
ACGTcount: A:0.16, C:0.34, G:0.33, T:0.16
Consensus pattern (106 bp):
GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
Found at i:28825 original size:11 final size:11
Alignment explanation
Indices: 28811--28842 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
28801 TCCCGGTGGT
28811 GCTCCGGCGAC
1 GCTCCGGCGAC
*
28822 GCTCCGGCGAT
1 GCTCCGGCGAC
28833 GCTCCGGCGA
1 GCTCCGGCGA
28843 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:36941 original size:33 final size:32
Alignment explanation
Indices: 36896--36977 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 32
36886 GTGTGCGTGC
* * *
36896 GCCTC-GTCACCATCGGTAATCCAAGGCGGGT
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGT
*
36927 GGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 -GCCTCGGTCACCATCGGCAAACCAAGACGGGT
36960 --CTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
36978 CCCCGACCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
30 18 0.40
32 5 0.11
33 22 0.49
ACGTcount: A:0.21, C:0.35, G:0.28, T:0.16
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAAACCAAGACGGGT
Found at i:37138 original size:32 final size:33
Alignment explanation
Indices: 37062--37146 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
37052 GTGTGCGTGA
* *
37062 GCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
37095 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
37127 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
37147 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:37272 original size:33 final size:33
Alignment explanation
Indices: 37230--37420 Score: 197
Period size: 33 Copynumber: 5.6 Consensus size: 33
37220 TTGTGCGTGA
*
37230 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
37263 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
* * * * *
37295 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG
**
37335 AGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
37369 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
37401 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
37421 CCCCCGGGCC
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:37273 original size:168 final size:169
Alignment explanation
Indices: 36760--37336 Score: 993
Period size: 168 Copynumber: 3.4 Consensus size: 169
36750 ACGTGTGCGT
**
36760 GCCTCGGTCACCATCGGCAAAAACAGACGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGG
36825 TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTGT
66 TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTGT
* *
36890 GCGTGCGCCTC-GTCACCATCGGTAATCCAAGGCGGGTG
131 GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
36928 GCCTCGGTCACCATCGGCAAACCCAGACGG-GTCTCGGTCACCATCGGCAACCCC-GACCATTGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGG
* *
36991 TGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTGT
66 TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTGT
37056 GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
131 GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
37095 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGAC-GGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* * *
37160 GTGCGGGAGTGCCGCACAGAACCGAGCGTT-GTGCGGGAGTCTCGGTCACCATCAGG-CCGCTTG
65 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
*
37223 TGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
130 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
37263 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGAC-GGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
37328 GTGCGGGAG
65 GTGCGGGAG
37337 CCTCGGTCAC
Statistics
Matches: 390, Mismatches: 15, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
166 81 0.21
167 78 0.20
168 147 0.38
169 49 0.13
170 35 0.09
ACGTcount: A:0.17, C:0.34, G:0.33, T:0.16
Consensus pattern (169 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGG
TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTGT
GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:37347 original size:106 final size:107
Alignment explanation
Indices: 37222--37443 Score: 410
Period size: 106 Copynumber: 2.1 Consensus size: 107
37212 CAGGCCGCTT
*
37222 GTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
*
37287 AGACGGGTGTCTCGGTCACCATCGGTAA-CCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCCGGGCCATTG
*
37328 GTGCGGGAGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
37393 AGACGGGTGTCTCGGTCACCATCGGCAACCCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCCGGGCCATTG
37435 GTGCGGGAG
1 GTGCGGGAG
37444 TGCCGCACAG
Statistics
Matches: 112, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
106 90 0.80
107 22 0.20
ACGTcount: A:0.16, C:0.35, G:0.33, T:0.16
Consensus pattern (107 bp):
GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
AGACGGGTGTCTCGGTCACCATCGGCAACCCCCGGGCCATTG
Found at i:37472 original size:106 final size:105
Alignment explanation
Indices: 37252--37512 Score: 332
Period size: 106 Copynumber: 2.5 Consensus size: 105
37242 ATCGGCAATC
*
37252 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGTAACC
1 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
** * *
37317 CCGGGCCATTGGTGCGGGAGCCTCGGTCACCATCGGCAGT
66 CCGGGCCATTGGTGCGGGAGCCTCGCACACAACCGGCAGT
37357 CCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAAC
1 -CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAA-
* *
37422 CCCCGGGCCATTGGTGCGGGAGTGC-CGCACAGAACCGGGC-GT
64 CCCCGGGCCATTGGTGCGGGAG-CCTCGCACACAACC-GGCAGT
** * * * *
37464 -TGGTGCGGG-AGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
1 CCAG-GCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
37513 CAACCCCAGG
Statistics
Matches: 138, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
105 37 0.27
106 67 0.49
107 30 0.22
108 4 0.03
ACGTcount: A:0.16, C:0.35, G:0.34, T:0.15
Consensus pattern (105 bp):
CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
CCGGGCCATTGGTGCGGGAGCCTCGCACACAACCGGCAGT
Found at i:37825 original size:11 final size:11
Alignment explanation
Indices: 37811--37842 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
37801 TCCCGGTGGT
37811 GCTCCGGCGAC
1 GCTCCGGCGAC
*
37822 GCTCCGGCGAT
1 GCTCCGGCGAC
37833 GCTCCGGCGA
1 GCTCCGGCGA
37843 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.