Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009435.1 Hibiscus syriacus cultivar Beakdansim tig00113491_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: 60960
ACGTcount: A:0.22, C:0.28, G:0.27, T:0.24
Found at i:6578 original size:32 final size:33
Alignment explanation
Indices: 6502--6586 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
6492 GTGTGCGTGC
* * *
6502 GCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
6535 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
6567 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
6587 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:6745 original size:32 final size:33
Alignment explanation
Indices: 6669--6753 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
6659 GTGTGCGTGA
* *
6669 GCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
6702 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
6734 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
6754 CCCCGGGCAT
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:6875 original size:32 final size:32
Alignment explanation
Indices: 6839--7028 Score: 170
Period size: 32 Copynumber: 5.7 Consensus size: 32
6829 TTGTGCGTGA
*
6839 GCCTCGGTCACCATCGGCAATCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAACCCAGGCGGGTG
* *
6871 GCCTCGGTCACCATCGGCAAACCAGACGGGT-
1 GCCTCGGTCACCATCGGCAACCCAGGCGGGTG
* * * *
6902 GTCTCGGTCACCATCGGTAACCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAACCCAGG-C----G-G-GTG
*
6941 AGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCA-ACCCAGGCGGGTG
**
6975 GCCTCGGTCACCATCGGCAAACCCAGAAGGGT-
1 GCCTCGGTCACCATCGGC-AACCCAGGCGGGTG
*
7007 GTCTCGGT-ACCATCGGCAACCC
1 GCCTCGGTCACCATCGGCAACCC
7029 CGGGCCATTG
Statistics
Matches: 130, Mismatches: 17, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
30 5 0.04
31 30 0.23
32 37 0.28
33 27 0.21
34 3 0.02
35 1 0.01
36 2 0.02
37 1 0.01
38 1 0.01
40 18 0.14
41 5 0.04
ACGTcount: A:0.18, C:0.35, G:0.32, T:0.16
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAACCCAGGCGGGTG
Found at i:6935 original size:168 final size:168
Alignment explanation
Indices: 6366--6942 Score: 975
Period size: 167 Copynumber: 3.4 Consensus size: 168
6356 ACGTGTGCGT
**
6366 GCCTCGGTCACCATCGGCAAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCGGGCCATTG
1 GCCTCGGTCACCATCGGC-AAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCGGGCCATTG
6431 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
65 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
* *
6496 GCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
130 GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
6535 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCGGGCCATTGG
* *
6600 TGCGGGAGTG-CGCACAGTA-CGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTGT
66 TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGG-CCCCGTGT
6663 GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
130 GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
6702 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGG-CATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAA-CCCGGGCCATTG
* * *
6766 GTGCGGGAGTGCCGCACAGAACCGAGCGCGTTGGTGCGGGAGTCTCGGTCACCATCAGGCCGCTT
65 GTGCGGGAGTGCCGCACAGAACCGA--GCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGT
6831 GTGCGTGAGCCTCGGTCACCATCGGCAATCC-AGGCGGGTG
128 GTGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
6871 GCCTCGGTCACCATCGGCAAA-CCAGACGGGTGTCTCGGTCACCATCGGTAACCCGGGCCATTGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCGGGCCATTGG
6935 TGCGGGAG
66 TGCGGGAG
6943 CCTCGGTCAC
Statistics
Matches: 387, Mismatches: 14, Indels: 15
0.93 0.03 0.04
Matches are distributed among these distances:
166 34 0.09
167 127 0.33
168 110 0.28
169 51 0.13
170 35 0.09
171 30 0.08
ACGTcount: A:0.17, C:0.33, G:0.34, T:0.16
Consensus pattern (168 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCGGGCCATTGG
TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGTG
CGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:6984 original size:33 final size:32
Alignment explanation
Indices: 6942--7025 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 32
6932 TGGTGCGGGA
** **
6942 GCCTCGGTCACCATCGGCAGTCCCAGGCGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGAAGGGT
6974 GGCCTCGGTCACCATCGGCAAACCCAGAAGGGT
1 -GCCTCGGTCACCATCGGCAAACCCAGAAGGGT
*
7007 GTCTCGGT-ACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
7026 CCCCGGGCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 11 0.24
32 7 0.15
33 28 0.61
ACGTcount: A:0.19, C:0.35, G:0.31, T:0.15
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAAACCCAGAAGGGT
Found at i:7019 original size:104 final size:104
Alignment explanation
Indices: 6831--7047 Score: 366
Period size: 104 Copynumber: 2.1 Consensus size: 104
6821 CAGGCCGCTT
*
6831 GTGCGTGAGCCTCGGTCACCATCGGCAATCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCAG
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCAG
* *
6896 ACGGGTGTCTCGGTCACCATCGGTAA-CCCGGGCCATTG
66 AAGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
*
6934 GTGCGGGAGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAAT-CCAGGCGGGTGGCCTCGGTCACCATCGGCAAA-CC
6999 AGAAGGGTGTCTCGGT-ACCATCGGCAACCCCGGGCCATTG
64 AGAAGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
7039 GTGCGGGAG
1 GTGCGGGAG
7048 TGCCGCACAG
Statistics
Matches: 107, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
103 27 0.25
104 42 0.39
105 38 0.36
ACGTcount: A:0.17, C:0.33, G:0.34, T:0.16
Consensus pattern (104 bp):
GTGCGGGAGCCTCGGTCACCATCGGCAATCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCAG
AAGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
Found at i:7427 original size:11 final size:11
Alignment explanation
Indices: 7411--7442 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
7401 TTCCCGTGGT
7411 GCTCCGGCGAC
1 GCTCCGGCGAC
*
7422 GCTCCGGCGAT
1 GCTCCGGCGAC
7433 GCTCCGGCGA
1 GCTCCGGCGA
7443 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:15536 original size:32 final size:33
Alignment explanation
Indices: 15460--15544 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
15450 GTGTGCGTGC
* * *
15460 GCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
15493 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
15525 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
15545 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:15606 original size:169 final size:170
Alignment explanation
Indices: 15323--15904 Score: 1051
Period size: 169 Copynumber: 3.4 Consensus size: 170
15313 ACGTGTGCGT
**
15323 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
15388 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* *
15453 TGCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
15493 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
15557 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
15622 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
15662 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* * *
15727 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG-CCGCTTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
*
15791 TGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
15831 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
15896 GTGCGGGAG
66 GTGCGGGAG
15905 CCTCGGTCAC
Statistics
Matches: 398, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
169 282 0.71
170 116 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:15705 original size:32 final size:33
Alignment explanation
Indices: 15629--15713 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
15619 GTGTGCGTGA
* *
15629 GCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
15662 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
15694 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
15714 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:15840 original size:33 final size:33
Alignment explanation
Indices: 15798--15988 Score: 197
Period size: 33 Copynumber: 5.6 Consensus size: 33
15788 TTGTGCGTGA
*
15798 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
15831 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
* * * * *
15863 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG
**
15903 AGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
15937 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
15969 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
15989 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:15872 original size:65 final size:66
Alignment explanation
Indices: 15798--15988 Score: 197
Period size: 65 Copynumber: 2.8 Consensus size: 66
15788 TTGTGCGTGA
*
15798 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
15863 -
66 G
* * * * * **
15863 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGGAGCCTCGGTCACCATCGGCAGTCCC
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG-GCCTCGGTCACCATCGGCAAACCC
*
15928 AGGCGGGTG
58 AGACGGGTG
* *
15937 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAA
15989 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:15915 original size:106 final size:106
Alignment explanation
Indices: 15790--16010 Score: 415
Period size: 106 Copynumber: 2.1 Consensus size: 106
15780 CAGGCCGCTT
*
15790 GTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
*
15855 AGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
*
15896 GTGCGGGAGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
15961 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
16002 GTGCGGGAG
1 GTGCGGGAG
16011 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:16393 original size:11 final size:11
Alignment explanation
Indices: 16379--16410 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
16369 TCCCGGTGGT
16379 GCTCCGGCGAC
1 GCTCCGGCGAC
*
16390 GCTCCGGCGAT
1 GCTCCGGCGAC
16401 GCTCCGGCGA
1 GCTCCGGCGA
16411 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:29061 original size:32 final size:33
Alignment explanation
Indices: 28985--29069 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
28975 GTGTGCGTGC
* * *
28985 GCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
29018 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
29050 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
29070 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:29131 original size:169 final size:170
Alignment explanation
Indices: 28848--29429 Score: 1051
Period size: 169 Copynumber: 3.4 Consensus size: 170
28838 ACGTGTGCGT
**
28848 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
28913 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* *
28978 TGCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
29018 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
29082 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
29147 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
29187 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* * *
29252 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG-CCGCTTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
*
29316 TGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
29356 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
29421 GTGCGGGAG
66 GTGCGGGAG
29430 CCTCGGTCAC
Statistics
Matches: 398, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
169 282 0.71
170 116 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:29230 original size:32 final size:33
Alignment explanation
Indices: 29154--29238 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
29144 GTGTGCGTGA
* *
29154 GCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
29187 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
29219 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
29239 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:29365 original size:33 final size:33
Alignment explanation
Indices: 29323--29513 Score: 197
Period size: 33 Copynumber: 5.6 Consensus size: 33
29313 TTGTGCGTGA
*
29323 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
29356 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
* * * * *
29388 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG
**
29428 AGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
29462 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
29494 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
29514 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:29397 original size:65 final size:66
Alignment explanation
Indices: 29323--29513 Score: 197
Period size: 65 Copynumber: 2.8 Consensus size: 66
29313 TTGTGCGTGA
*
29323 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
29388 -
66 G
* * * * * **
29388 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGGAGCCTCGGTCACCATCGGCAGTCCC
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG-GCCTCGGTCACCATCGGCAAACCC
*
29453 AGGCGGGTG
58 AGACGGGTG
* *
29462 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAA
29514 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:29440 original size:106 final size:106
Alignment explanation
Indices: 29315--29535 Score: 415
Period size: 106 Copynumber: 2.1 Consensus size: 106
29305 CAGGCCGCTT
*
29315 GTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
*
29380 AGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
*
29421 GTGCGGGAGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
29486 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
29527 GTGCGGGAG
1 GTGCGGGAG
29536 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:29919 original size:11 final size:11
Alignment explanation
Indices: 29905--29936 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
29895 TCCCGGTGGT
29905 GCTCCGGCGAC
1 GCTCCGGCGAC
*
29916 GCTCCGGCGAT
1 GCTCCGGCGAC
29927 GCTCCGGCGA
1 GCTCCGGCGA
29937 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:42590 original size:32 final size:33
Alignment explanation
Indices: 42514--42598 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
42504 GTGTGCGTGC
* * *
42514 GCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
42547 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
42579 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
42599 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:42660 original size:169 final size:170
Alignment explanation
Indices: 42377--42958 Score: 1051
Period size: 169 Copynumber: 3.4 Consensus size: 170
42367 ACGTGTGCGT
**
42377 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
42442 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* *
42507 TGCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
42547 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
42611 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
42676 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
42716 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* * *
42781 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG-CCGCTTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
*
42845 TGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
42885 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
42950 GTGCGGGAG
66 GTGCGGGAG
42959 CCTCGGTCAC
Statistics
Matches: 398, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
169 282 0.71
170 116 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:42759 original size:32 final size:33
Alignment explanation
Indices: 42683--42767 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
42673 GTGTGCGTGA
* *
42683 GCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
42716 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
42748 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
42768 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:42894 original size:33 final size:33
Alignment explanation
Indices: 42852--43042 Score: 197
Period size: 33 Copynumber: 5.6 Consensus size: 33
42842 TTGTGCGTGA
*
42852 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
42885 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
* * * * *
42917 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG
**
42957 AGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
42991 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
43023 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
43043 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:42926 original size:65 final size:66
Alignment explanation
Indices: 42852--43042 Score: 197
Period size: 65 Copynumber: 2.8 Consensus size: 66
42842 TTGTGCGTGA
*
42852 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
42917 -
66 G
* * * * * **
42917 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGGAGCCTCGGTCACCATCGGCAGTCCC
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG-GCCTCGGTCACCATCGGCAAACCC
*
42982 AGGCGGGTG
58 AGACGGGTG
* *
42991 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAA
43043 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:42969 original size:106 final size:106
Alignment explanation
Indices: 42844--43064 Score: 415
Period size: 106 Copynumber: 2.1 Consensus size: 106
42834 CAGGCCGCTT
*
42844 GTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
*
42909 AGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
*
42950 GTGCGGGAGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
43015 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
43056 GTGCGGGAG
1 GTGCGGGAG
43065 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:43448 original size:11 final size:11
Alignment explanation
Indices: 43434--43465 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
43424 TCCCGGTGGT
43434 GCTCCGGCGAC
1 GCTCCGGCGAC
*
43445 GCTCCGGCGAT
1 GCTCCGGCGAC
43456 GCTCCGGCGA
1 GCTCCGGCGA
43466 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.