Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009484.1 Hibiscus syriacus cultivar Beakdansim tig00114536_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: 29752
ACGTcount: A:0.23, C:0.27, G:0.29, T:0.22
Found at i:1677 original size:33 final size:32
Alignment explanation
Indices: 1638--1724 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 32
1628 CGTGAGCCCC
*
1638 GTCACCATCGGCAATCCCAGGCGGGTGGCCTCG
1 GTCACCATCGGCAAACCCAGGCGGGT-GCCTCG
* ** *
1671 GTCACCATCGGCAAAACCATACGGGTGTCTCG
1 GTCACCATCGGCAAACCCAGGCGGGTGCCTCG
*
1703 GTCACCATCGGCAACCCCAGGC
1 GTCACCATCGGCAAACCCAGGC
1725 CATTGGTGAG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 23 0.51
33 22 0.49
ACGTcount: A:0.21, C:0.37, G:0.28, T:0.15
Consensus pattern (32 bp):
GTCACCATCGGCAAACCCAGGCGGGTGCCTCG
Found at i:1708 original size:32 final size:33
Alignment explanation
Indices: 1638--1716 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
1628 CGTGAGCCCC
** *
1638 GTCACCATCGGCAATCCCAGGCGGGTGGCCTCG
1 GTCACCATCGGCAAAACCAGACGGGTGGCCTCG
* *
1671 GTCACCATCGGCAAAACCATACGGGT-GTCTCG
1 GTCACCATCGGCAAAACCAGACGGGTGGCCTCG
1703 GTCACCATCGGCAA
1 GTCACCATCGGCAA
1717 CCCCAGGCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 19 0.46
33 22 0.54
ACGTcount: A:0.22, C:0.34, G:0.28, T:0.16
Consensus pattern (33 bp):
GTCACCATCGGCAAAACCAGACGGGTGGCCTCG
Found at i:1854 original size:31 final size:31
Alignment explanation
Indices: 1771--1900 Score: 174
Period size: 32 Copynumber: 4.2 Consensus size: 31
1761 GTGCGTGAGG
* *
1771 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATC-GCAAACCCAGACGGGT-GT
1803 CTCGGTCACCATCGCAAACCCAGAC-GGTGT
1 CTCGGTCACCATCGCAAACCCAGACGGGTGT
1833 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATC-GCAAACCCAGACGGGTGT
* * *
1865 CTCGGTCACCATCGCAACCCCCGACGGGTGG
1 CTCGGTCACCATCGCAAACCCAGACGGGTGT
1896 CTCGG
1 CTCGG
1901 CAACCCCAGG
Statistics
Matches: 90, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
30 14 0.16
31 37 0.41
32 39 0.43
ACGTcount: A:0.18, C:0.38, G:0.29, T:0.15
Consensus pattern (31 bp):
CTCGGTCACCATCGCAAACCCAGACGGGTGT
Found at i:1869 original size:62 final size:63
Alignment explanation
Indices: 1769--1900 Score: 196
Period size: 62 Copynumber: 2.1 Consensus size: 63
1759 TGGTGCGTGA
*
1769 GGCTCGGTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGCAAACCCAGAC-GGT
1 GGCTCGGTCACCATCGGCAACCCAGACGGGTGGCCTCGGTCACCATCGCAAACCCAGACGGGT
* * * *
1831 GTCTCGGTCACCATCGGCAAACCCAGACGGGT-GTCTCGGTCACCATCGCAACCCCCGACGGGT
1 GGCTCGGTCACCATCGGC-AACCCAGACGGGTGGCCTCGGTCACCATCGCAAACCCAGACGGGT
1894 GGCTCGG
1 GGCTCGG
1901 CAACCCCAGG
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
62 41 0.66
63 21 0.34
ACGTcount: A:0.18, C:0.37, G:0.30, T:0.14
Consensus pattern (63 bp):
GGCTCGGTCACCATCGGCAACCCAGACGGGTGGCCTCGGTCACCATCGCAAACCCAGACGGGT
Found at i:2049 original size:64 final size:63
Alignment explanation
Indices: 1949--2084 Score: 222
Period size: 64 Copynumber: 2.1 Consensus size: 63
1939 CCGAGAGTTT
1949 GGGTGCGGGGTCCTCGTTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGTCCTCGTTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
*
2012 -GGTGCGGGG-CCTCGTCATCACCATCCGGCAACCCCCGACGGGTGCCTCGTCAACCCCAGGCCA
1 GGGTGCGGGGTCCTCGT--TCACCAT-CGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCA
2075 C
63 C
2076 GGGTGCGGG
1 GGGTGCGGG
2085 AGTGCCGCAC
Statistics
Matches: 68, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
61 6 0.09
62 9 0.13
63 7 0.10
64 38 0.56
65 8 0.12
ACGTcount: A:0.14, C:0.40, G:0.33, T:0.12
Consensus pattern (63 bp):
GGGTGCGGGGTCCTCGTTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
Found at i:2068 original size:161 final size:157
Alignment explanation
Indices: 1870--2156 Score: 400
Period size: 161 Copynumber: 1.8 Consensus size: 157
1860 GGTGTCTCGG
* * *
1870 TCACCATCGCAACCCCCGACGGGTGGCTCGGCAACCCCAGGCCACGGGTGCGGGAGTTTCCGGAC
1 TCACCATCGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAG-TGCCGCAC
* * *
1935 AGAGCCGAGAGTTTGGGTGCG-G-GGTCCTCGTTCACCATCGGCAACCCCCGACGGGT-GCCTCG
65 AGAACCGAGAG-TT-GGTGCGTGAGG--CTCGGTCACCATCGGCAACCCCAGACGGGTGGCCTCG
1997 GCAACCCCAGGCCACGGTGCGGGGCCTCGTCA
126 GCAACCCCAGGCCACGGTGCGGGGCCTCGTCA
*
2029 TCACCATCCGGCAACCCCCGACGGGTGCCTCGTCAACCCCAGGCCACGGGTGCGGGAGTGCCGCA
1 TCACCAT-C-GCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCA
* * *
2094 CAGAACCGAGCGTTGGTGCGTGAGGCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGG
64 CAGAACCGAGAGTTGGTGCGTGAGGCTCGGTCACCATCGGCAACCCCAGACGGGTGGCCTCGG
2157 TCACCATTGC
Statistics
Matches: 113, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
158 32 0.28
159 17 0.15
160 18 0.16
161 46 0.41
ACGTcount: A:0.16, C:0.36, G:0.34, T:0.14
Consensus pattern (157 bp):
TCACCATCGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCACA
GAACCGAGAGTTGGTGCGTGAGGCTCGGTCACCATCGGCAACCCCAGACGGGTGGCCTCGGCAAC
CCCAGGCCACGGTGCGGGGCCTCGTCA
Found at i:2201 original size:32 final size:32
Alignment explanation
Indices: 2119--2249 Score: 169
Period size: 32 Copynumber: 4.2 Consensus size: 32
2109 GTGCGTGAGG
* *
2119 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
2152 CTCGGTCACCAT-TGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
2183 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
2215 CTC-GTCACCATCGGC-AACCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
2245 CTCGG
1 CTCGG
2250 CAACCCCAGG
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
30 16 0.18
31 26 0.30
32 33 0.38
33 12 0.14
ACGTcount: A:0.18, C:0.36, G:0.30, T:0.16
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:2219 original size:158 final size:158
Alignment explanation
Indices: 1800--2221 Score: 445
Period size: 158 Copynumber: 2.7 Consensus size: 158
1790 CCAGGCGGGT
* *
1800 GGCCTCGGTCACCATC-GCAAACCCAGAC-GGTGTCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GGCCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCAT--GCAAAGCCAGACGGGT
* *
1863 GTCTCGGTCACCATC-GCAACCCCCGACGGGTGGCTCGGCAACCCCAGGCCACGGGTGCGGGAGT
64 GTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGTCAACCCCAGGCCACGGGTGCGGGAGT
* * *
1927 TTCCGGACAGAGCCGAGAGTTTGGGTGCGG
129 TGCCGCACAGAACCGAGAGTTTGGGTGCGG
* * * * * *
1957 GGTCCTCGTTCACCATCGGCAACCCCCGACGGGTGCCTCGG-CAACC---CCAGGCCACGGTGCG
1 GG-CCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTC-ACCATGCAAAGCCA--G-ACG
* *
2018 GG-GCCTCGTCATCACCATCCGGCAACCCCCGACGGGTGCCTCGTCAACCCCAGGCCACGGGTGC
61 GGTGTCTCG--GTCACCAT-CGGCAACCCCCGACGGGTGCCTCGTCAACCCCAGGCCACGGGTGC
*
2082 GGGAG-TGCCGCACAGAACCGAGCG-TT-GGTGCGTG
123 GGGAGTTGCCGCACAGAACCGAGAGTTTGGGTGCG-G
* *
2116 AGG-CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGCAAAGCCAGACGGG
1 -GGCCTCGGTCACCATCGGCAAACCCAGACGGGT-GCCTCGGTCACCA-TGCAAAGCCAGACGGG
* * *
2180 TGTCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGTCA
63 TGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGTCA
2222 CCATCGGCAA
Statistics
Matches: 217, Mismatches: 28, Indels: 39
0.76 0.10 0.14
Matches are distributed among these distances:
155 5 0.02
157 8 0.04
158 73 0.34
159 38 0.18
160 35 0.16
161 52 0.24
163 6 0.03
ACGTcount: A:0.18, C:0.36, G:0.32, T:0.15
Consensus pattern (158 bp):
GGCCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATGCAAAGCCAGACGGGTGT
CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGTCAACCCCAGGCCACGGGTGCGGGAGTTG
CCGCACAGAACCGAGAGTTTGGGTGCGG
Found at i:2334 original size:89 final size:92
Alignment explanation
Indices: 2215--2380 Score: 268
Period size: 89 Copynumber: 1.8 Consensus size: 92
2205 AGACGGGTGT
2215 CTCGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCA-CGGTGC-GGAGTGCCG
1 CTCGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCATCGGTGCGGGAGTGCCG
*
2278 CACAGAGCCGAGAGTTTGGGTGCGGGC
66 CACAGAACCGAGAGTTTGGGTGCGGGC
* *
2305 CTCGTCACCATC-GC-ACACCCGACGGGTGCCTCGGCAACCCCAGTCCATTGGTGCGGGAGTGCC
1 CTCGTCACCATCGGCAAC-CCCGACGGGTGCCTCGGCAACCCCAGGCCATCGGTGCGGGAGTGCC
2368 GCACAGAACCGAG
65 GCACAGAACCGAG
2381 CGCTGGGTTG
Statistics
Matches: 70, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
88 2 0.03
89 31 0.44
90 17 0.24
91 20 0.29
ACGTcount: A:0.18, C:0.37, G:0.33, T:0.13
Consensus pattern (92 bp):
CTCGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCATCGGTGCGGGAGTGCCG
CACAGAACCGAGAGTTTGGGTGCGGGC
Found at i:10536 original size:31 final size:32
Alignment explanation
Indices: 10496--10582 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 32
10486 GCGTGAGCCC
*
10496 CGGTCACCATCGGCAATCCCAGGC-GGTGGCCT
1 CGGTCACCATCGGCAAACCCAGGCGGGT-GCCT
* ** *
10528 C-GTCACCATCGGCAAAACCATACGGGTGTCT
1 CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
*
10559 CGGTCACCATCGGCAACCCCAGGC
1 CGGTCACCATCGGCAAACCCAGGC
10583 CATTGGTGAG
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
31 22 0.50
32 22 0.50
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (32 bp):
CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
Found at i:10670 original size:32 final size:32
Alignment explanation
Indices: 10629--10742 Score: 194
Period size: 32 Copynumber: 3.6 Consensus size: 32
10619 GTGCGTGAGG
* *
10629 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
10661 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
10693 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
10725 CTCGGTCACCATCGGCAA
1 CTCGGTCACCATCGGCAA
10743 CCCCCGGGTG
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
32 67 0.85
33 12 0.15
ACGTcount: A:0.20, C:0.36, G:0.29, T:0.15
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:10925 original size:62 final size:63
Alignment explanation
Indices: 10817--10934 Score: 229
Period size: 62 Copynumber: 1.9 Consensus size: 63
10807 GTGCGGTCCC
10817 GTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCG
1 GTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCG
10880 GTCACCATCGGCAACCCCCGAC-GGTGCCTCGGCAACCCCAGGCCACGGGTGCGGG
1 GTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGG
10935 AGTGCCGCAC
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 33 0.60
63 22 0.40
ACGTcount: A:0.15, C:0.42, G:0.34, T:0.09
Consensus pattern (63 bp):
GTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCG
Found at i:11076 original size:31 final size:32
Alignment explanation
Indices: 10969--11092 Score: 160
Period size: 32 Copynumber: 3.9 Consensus size: 32
10959 GTGCGTGAGG
* * * *
10969 CTCGGTCACCATCGGCAATCCCAGGCGTGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
* *
11002 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
11034 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* *
11066 CTC-GTCACCATCGGCAACCCCCGACGG
1 CTCGGTCACCATCGGCAAACCCAGACGG
11093 TGCCTCGCAA
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
31 22 0.27
32 34 0.42
33 25 0.31
ACGTcount: A:0.19, C:0.36, G:0.28, T:0.16
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:11136 original size:340 final size:343
Alignment explanation
Indices: 10568--11216 Score: 1094
Period size: 340 Copynumber: 1.9 Consensus size: 343
10558 TCGGTCACCA
**
10568 TCGGCAACCCCAGGCCATTGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
1 TCGGCAACCCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
10633 GTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
66 GTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
*
10698 TCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGGGTGGCTCGGCAAC
131 TCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGGGTGCCTCGGCAAC
* * *
10763 CCCAGGCCACGGGTGCGGGAGTTCCGGACAGAGCCGAGAGTTGGGTGC-GGTCC-C-GTCACCAT
196 CCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGCCTCGGTCACCAT
*
10825 CGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACCATCG
261 CGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACCATCG
10890 GCAACCCCCGACGGTGCC
326 GCAACCCCCGACGGTGCC
*
10908 TCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
1 TCGGCAACCCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
* * *
10973 GTCACCATCGGCAATCCCAGGCGTGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGTCTCG
66 GTCACCATCGGCAA-CCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCG
11038 GTCACCATCGGCAAACCCAGACGGGTGTCTC-GTCACCATCGGCAACCCCCGACGGTGCCTC-GC
130 GTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCG--GGTGCCTCGGC
11101 AACCCCAGGCCAC-GGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCA
193 AACCCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGC-GGGGCCTCGGTCA
* **
11165 CCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGTCCATTGGTGCGGG
257 CCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGG
11217 AGTGCCGCAC
Statistics
Matches: 288, Mismatches: 14, Indels: 10
0.92 0.04 0.03
Matches are distributed among these distances:
340 131 0.45
341 93 0.32
342 11 0.04
343 1 0.00
344 52 0.18
ACGTcount: A:0.18, C:0.35, G:0.34, T:0.13
Consensus pattern (343 bp):
TCGGCAACCCCAGGCCACGGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
GTCACCATCGGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
TCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGGGTGCCTCGGCAAC
CCCAGGCCACGGGTGCGGGAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGCCTCGGTCACCAT
CGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACCATCG
GCAACCCCCGACGGTGCC
Found at i:19336 original size:32 final size:31
Alignment explanation
Indices: 19297--19380 Score: 98
Period size: 32 Copynumber: 2.7 Consensus size: 31
19287 TTGAGCCCCG
*
19297 GTCACCATCGGCAATCCCAGGCGGGTGGCCTC
1 GTCACCATCGGCAAACCCAGGCGGGT-GCCTC
* ** *
19329 GTCACCATCGGCAAAACCATACGGGTGTCTC
1 GTCACCATCGGCAAACCCAGGCGGGTGCCTC
*
19360 GTCACCATC-GCAACCCCAGGC
1 GTCACCATCGGCAAACCCAGGC
19381 CATTGGTGAG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
30 8 0.19
31 13 0.30
32 22 0.51
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.15
Consensus pattern (31 bp):
GTCACCATCGGCAAACCCAGGCGGGTGCCTC
Found at i:19494 original size:30 final size:31
Alignment explanation
Indices: 19427--19553 Score: 156
Period size: 30 Copynumber: 4.2 Consensus size: 31
19417 GTGCGTGAGG
* *
19427 CTCGGTCACCATC-GCAACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAACCCAGACGGGT-GT
19458 CTCGGTCACCATC-GCAAACCCAGAC-GGTGT
1 CTCGGTCACCATCGGC-AACCCAGACGGGTGT
19488 CTCGGTCACCATCGGCAACCCAGAC-GGTGT
1 CTCGGTCACCATCGGCAACCCAGACGGGTGT
* *
19518 CTC-GTCACCATCGGCAACCCCCGACGGGTGG
1 CTCGGTCACCATCGGCAA-CCCAGACGGGTGT
19549 CTCGG
1 CTCGG
19554 CAACCCCAGG
Statistics
Matches: 87, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
29 14 0.16
30 37 0.43
31 27 0.31
32 9 0.10
ACGTcount: A:0.18, C:0.39, G:0.28, T:0.15
Consensus pattern (31 bp):
CTCGGTCACCATCGGCAACCCAGACGGGTGT
Found at i:19553 original size:61 final size:61
Alignment explanation
Indices: 19425--19553 Score: 165
Period size: 61 Copynumber: 2.1 Consensus size: 61
19415 TGGTGCGTGA
*
19425 GGCTCGGTCACCATCGCAACCCAGGCGGGTGGCCTCGGTCACCATCGCAAACCCAGACGGT
1 GGCTCGGTCACCATCGCAACCCAGACGGGTGGCCTCGGTCACCATCGCAAACCCAGACGGT
* * * *
19486 GTCTCGGTCACCATCGGCAACCCAGAC-GGT-GTCTC-GTCACCATCGGCAACCCCCGACGGGT
1 GGCTCGGTCACCATC-GCAACCCAGACGGGTGGCCTCGGTCACCATC-GCAAACCCAGAC-GGT
19547 GGCTCGG
1 GGCTCGG
19554 CAACCCCAGG
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
59 9 0.15
60 14 0.24
61 26 0.44
62 10 0.17
ACGTcount: A:0.18, C:0.38, G:0.29, T:0.15
Consensus pattern (61 bp):
GGCTCGGTCACCATCGCAACCCAGACGGGTGGCCTCGGTCACCATCGCAAACCCAGACGGT
Found at i:19699 original size:56 final size:57
Alignment explanation
Indices: 19600--19723 Score: 166
Period size: 58 Copynumber: 2.1 Consensus size: 57
19590 GCCGAGAGTT
19600 GGTGCGGGGGTCCTCGTCACCATCGAACCCCCGACGGGTGCCT-CAACCCCAGGCCACG
1 GGTGC-GGGGTCCTCGTCACCATCGAACCCCCGACGGGTGCCTGCAACCCCA-GCCACG
19658 GGTGCGGGG-CCTCGTCACCATCGGCAACCCCCGAC-GG-GCCTCGGCAACCCCAGCCACG
1 GGTGCGGGGTCCTCGTCACCATC-G-AACCCCCGACGGGTGCCT--GCAACCCCAGCCACG
19716 GGTGCGGG
1 GGTGCGGG
19724 AGTGCCGCAC
Statistics
Matches: 61, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
56 17 0.28
57 7 0.11
58 29 0.48
59 8 0.13
ACGTcount: A:0.15, C:0.41, G:0.34, T:0.10
Consensus pattern (57 bp):
GGTGCGGGGTCCTCGTCACCATCGAACCCCCGACGGGTGCCTGCAACCCCAGCCACG
Found at i:19796 original size:31 final size:29
Alignment explanation
Indices: 19758--19886 Score: 125
Period size: 31 Copynumber: 4.2 Consensus size: 29
19748 GTGCGTGAGG
* *
19758 CTCGTCACCATCGGCAATCCCGGCGGGTGGC
1 CTCGTCACCATCGGCAAACCCGAC-GGT-GC
* * *
19789 CTCGTCACCATTGGCAAAGCCAGACGGTGT
1 CTCGTCACCATCGGCAAA-CCCGACGGTGC
*
19819 CTCGGTCACCATCGGCAAACCCAGACGGTGT
1 CTC-GTCACCATCGGCAAACCC-GACGGTGC
*
19850 CTCGGTCACCATCGGCAACCCCGACGGGTGC
1 CTC-GTCACCATCGGCAAACCCGAC-GGTGC
19881 C-CGTCA
1 CTCGTCA
19887 ACCCCAGGCC
Statistics
Matches: 85, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
29 4 0.05
30 10 0.12
31 67 0.79
32 4 0.05
ACGTcount: A:0.19, C:0.37, G:0.28, T:0.16
Consensus pattern (29 bp):
CTCGTCACCATCGGCAAACCCGACGGTGC
Found at i:28124 original size:33 final size:32
Alignment explanation
Indices: 28084--28170 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 32
28074 CGTGAGCCCC
*
28084 GTCACCATCGGCAATCCCAGGCGGGTGGCCTCG
1 GTCACCATCGGCAAACCCAGGCGGGT-GCCTCG
* ** *
28117 GTCACCATCGGCAAAACCATACGGGTGTCTCG
1 GTCACCATCGGCAAACCCAGGCGGGTGCCTCG
*
28149 GTCACCATCGGCAACCCCAGGC
1 GTCACCATCGGCAAACCCAGGC
28171 CATTGGTGAG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 23 0.51
33 22 0.49
ACGTcount: A:0.21, C:0.37, G:0.28, T:0.15
Consensus pattern (32 bp):
GTCACCATCGGCAAACCCAGGCGGGTGCCTCG
Found at i:28154 original size:32 final size:33
Alignment explanation
Indices: 28084--28162 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
28074 CGTGAGCCCC
** *
28084 GTCACCATCGGCAATCCCAGGCGGGTGGCCTCG
1 GTCACCATCGGCAAAACCAGACGGGTGGCCTCG
* *
28117 GTCACCATCGGCAAAACCATACGGGT-GTCTCG
1 GTCACCATCGGCAAAACCAGACGGGTGGCCTCG
28149 GTCACCATCGGCAA
1 GTCACCATCGGCAA
28163 CCCCAGGCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 19 0.46
33 22 0.54
ACGTcount: A:0.22, C:0.34, G:0.28, T:0.16
Consensus pattern (33 bp):
GTCACCATCGGCAAAACCAGACGGGTGGCCTCG
Found at i:28282 original size:31 final size:32
Alignment explanation
Indices: 28217--28345 Score: 178
Period size: 31 Copynumber: 4.2 Consensus size: 32
28207 GTGCGTGAGG
*
28217 CTCGGTCACCATCGGC-AACCCAG-C-GGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
28247 CTCGGTCACCATCGGCAAACCCAGAC-GGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
28278 CTCGGTCACCATC-GCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* * *
28309 CTCGGTCACCATCGGCAACCCCCGACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
28341 CTCGG
1 CTCGG
28346 CAACCCCAGG
Statistics
Matches: 91, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
30 28 0.31
31 39 0.43
32 24 0.26
ACGTcount: A:0.19, C:0.38, G:0.29, T:0.15
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:28512 original size:59 final size:58
Alignment explanation
Indices: 28396--28518 Score: 185
Period size: 63 Copynumber: 2.1 Consensus size: 58
28386 AGAGTTGGGT
*
28396 GGGGTCCTCGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGC
1 GGGGGCCTCGTCACCATCGGCAACCCCCGAC--G-GCCTCGGCAACCCCAGGCCAC-GGTGC
28458 GGGGGCCTCGGTCACCATCGGCAACCCCCGAC-GCCTCGGCAACCCCAGGCCACGGTGC
1 GGGGGCCTC-GTCACCATCGGCAACCCCCGACGGCCTCGGCAACCCCAGGCCACGGTGC
28516 GGG
1 GGG
28519 AGTGCCGCAC
Statistics
Matches: 59, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
58 8 0.14
59 21 0.36
62 8 0.14
63 22 0.37
ACGTcount: A:0.15, C:0.42, G:0.33, T:0.10
Consensus pattern (58 bp):
GGGGGCCTCGTCACCATCGGCAACCCCCGACGGCCTCGGCAACCCCAGGCCACGGTGC
Found at i:28639 original size:155 final size:153
Alignment explanation
Indices: 28246--28645 Score: 440
Period size: 154 Copynumber: 2.6 Consensus size: 153
28236 CCAGCGGTGG
* * *
28246 CCTCGGTCACCATCGGCAAACCCAGAC-GGTGTCTCGGTCACCATCGCAAACCCAGACGGGTGTC
1 CCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATGGCAAAGCCAGACGGGTGTC
* *
28310 TCGGTCACCATCGGCAACCCCCGACGGGTGGCTCGGCAACCCCAGGCCACGGGTGCGGGAGTTCC
66 TCGGTCACCATCGGCAACCCCCGAC--G-GCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCC
* *
28375 GGACAGAGCCGAGAGTTGGGTGGGGT
128 GCACAGAACCGAGAGTTGGGTGGGGT
* * * * *** *
28401 CCTC-GTCACCATCGGCAACCCCCGACGGGTGCCTCGG-CAACCCCA-GGCCACGGGTG-CGGGG
1 CCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTC-A--CCATGGCAAAGCCAGACGGGT
*
28462 GCCTCGGTCACCATCGGCAACCCCCGAC-GCCTCGGCAACCCCAGGCCAC-GGTGCGGGAGTGCC
63 GTCTCGGTCACCATCGGCAACCCCCGACGGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCC
*
28525 GCACAGAACCGAGCGTT-GGTGCGTGAG-
128 GCACAGAACCGAGAGTTGGGTG-G-G-GT
* * *
28552 GCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTG
1 CCTCGGTCACCATCGGCAAACCCAGACGGGT-GCCTCGGTCACCA-TGGCAAAGCCAGACGGGTG
* *
28617 TCTCGGTCACCATCGGCAAACCCAGACGG
64 TCTCGGTCACCATCGGCAACCCCCGACGG
28646 TGTCTCGGTC
Statistics
Matches: 201, Mismatches: 30, Indels: 28
0.78 0.12 0.11
Matches are distributed among these distances:
149 4 0.02
150 28 0.14
151 27 0.13
152 24 0.12
153 14 0.07
154 51 0.25
155 46 0.23
156 4 0.02
157 3 0.01
ACGTcount: A:0.18, C:0.36, G:0.33, T:0.13
Consensus pattern (153 bp):
CCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATGGCAAAGCCAGACGGGTGTC
TCGGTCACCATCGGCAACCCCCGACGGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCCGCA
CAGAACCGAGAGTTGGGTGGGGT
Found at i:28651 original size:31 final size:32
Alignment explanation
Indices: 28553--28684 Score: 169
Period size: 31 Copynumber: 4.2 Consensus size: 32
28543 GTGCGTGAGG
* *
28553 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
28586 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
28618 CTCGGTCACCATCGGCAAACCCAGAC-GGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
* *
28649 CTCGGTCACCATCGGCAACCCCCGAC-GGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
28680 CTCGG
1 CTCGG
28685 CAACCCCAGG
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 38 0.43
32 25 0.28
33 26 0.29
ACGTcount: A:0.18, C:0.36, G:0.30, T:0.16
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:28779 original size:336 final size:334
Alignment explanation
Indices: 28156--28796 Score: 1033
Period size: 336 Copynumber: 1.9 Consensus size: 334
28146 TCGGTCACCA
*
28156 TCGGCAACCCCAGGCCATTGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
1 TCGGCAACCCCAGGCCATCGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
28221 GTCACCATCGGCAACCCAGCGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCA
66 GTCACCATCGGCAACCCAGCGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCA
*
28286 CCATCGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGGCTCGGCAACC
131 CCATCGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACC
* * *
28351 CCAGGCCACGGGTGCGGGAGTTCCGGACAGAGCCGAGAGTTGGGTGGGGTCCTCGTCACCATCGG
196 CCAGGCCACGGGT---GGAGTGCCGCACAGAGCCGAGAGTTGGGTGGGGGCCTCGTCACCATCGG
*
28416 CAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACCATCGGCA
258 CAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACCATCGGCA
28481 ACCCCCGACGCC
323 ACCCCCGACGCC
*
28493 TCGGCAACCCCAGGCCA-CGGTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
1 TCGGCAACCCCAGGCCATCGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
* *
28557 GTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGTCTCG
66 GTCACCATCGGCAA-CCCA-GC-GGTGGCCTCGGTCACCATCGGCAAACCCAGAC-GGTGTCTCG
28622 GTCACCATCGGCAAACCCAGAC-GGTGTCTCGGTCACCATCGGCAACCCCCGAC-GGTGCCTCGG
127 GTCACCATC-GCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
28685 CAACCCCAGGCCAC-GGT-GAGTGCCGCACAGAGCCGAGAGTTGGGTGCGGGGGCCTCGGTCACC
191 CAACCCCAGGCCACGGGTGGAGTGCCGCACAGAGCCGAGAGTTGGGT--GGGGGCCTC-GTCACC
* **
28748 ATCGGCAACACCCGACGGGTGCCTC-GCAACCCCAGTCCATTGGTGCGGG
253 ATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGG
28797 TGCCGCACAG
Statistics
Matches: 284, Mismatches: 12, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
334 26 0.09
336 88 0.31
337 51 0.18
338 5 0.02
339 53 0.19
340 49 0.17
341 12 0.04
ACGTcount: A:0.18, C:0.35, G:0.33, T:0.13
Consensus pattern (334 bp):
TCGGCAACCCCAGGCCATCGGTGAGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGTGAGGCTCG
GTCACCATCGGCAACCCAGCGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCA
CCATCGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACC
CCAGGCCACGGGTGGAGTGCCGCACAGAGCCGAGAGTTGGGTGGGGGCCTCGTCACCATCGGCAA
CACCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGGCCTCGGTCACCATCGGCAACC
CCCGACGCC
Done.