Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009510.1 Hibiscus syriacus cultivar Beakdansim tig00115348_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: 21384
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Found at i:1725 original size:31 final size:32
Alignment explanation
Indices: 1651--1781 Score: 169
Period size: 31 Copynumber: 4.2 Consensus size: 32
1641 GCCTGGGTTG
*
1651 CCGAGGCACCCGTC-GGG-TTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1681 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
1713 CCGAGACA-CCGTCTGGCTTTGCCAATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* * * *
1744 CCGAGGCCACCCGCCTGTGATTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
1777 CCGAG
1 CCGAG
1782 CCTCACGCAC
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
30 13 0.15
31 28 0.32
32 25 0.28
33 22 0.25
ACGTcount: A:0.16, C:0.31, G:0.34, T:0.19
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Found at i:1861 original size:156 final size:155
Alignment explanation
Indices: 1681--2096 Score: 452
Period size: 156 Copynumber: 2.7 Consensus size: 155
1671 CCGATGGTGA
*
1681 CCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCGTCTGGCTTTGCCAATGGTGACC
1 CCGAGACACCCGTC-GGGGTTGCCGATGGTGACCGAGACACCGTCTGGCTTTGCCAATGGTGACC
* * * *
1746 GAGGCCACCCGCCTGTGATTGCCGATGGTGACCGAG-CCTCACGCA-CCAACGCTCGGTTCTGTG
65 GAGG-CACCCGTCTGGGATTGCCGATGGTGACCGAGACC-C-CGCACCCAACGCTCGGCTCTGTC
1809 CGCACTCCCGCACCCGTGGCCTGGGGTTG
127 CGCACTCCCGCACCCGTGGCCTGGGGTTG
* * *** *** ***
1838 CCGAG-CACCCGTCGGGGGTTGCCGATGGTGACCGAGGCCCCCG-CACCCCCGGCCTGGGGTTG-
1 CCGAGACACCCGTC-GGGGTTGCCGATGGTGACCGA-GACACCGTCTGGCTTTGCCAATGG-TGA
* * *
1900 CCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGACCCCGCACCCAACTCTCGGCTCTGTC
63 CCGAGGCACCCGTCTGGGATTGCCGATGGTGACCGA-GACCCCGCACCCAACGCTCGGCTCTGTC
*
1965 CGGACTCCCGCACCCGTGGCCTGGGGTTG
127 CGCACTCCCGCACCCGTGGCCTGGGGTTG
* * *
1994 CCGAGCCACCCGTCGGGGTTGCCGA---TGACCGAGACACCCGTCTGGTTTTGCCGATGGTGACC
1 CCGAGACACCCGTCGGGGTTGCCGATGGTGACCGAGACA-CCGTCTGGCTTTGCCAATGGTGA-C
* * *
2056 CGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGCCCC
64 CGAGGCACCCGTCTGGGATTGCCGATGGTGACCGAGACCCC
2097 CCGCCTGGGT
Statistics
Matches: 212, Mismatches: 37, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
152 2 0.01
153 12 0.06
154 11 0.05
155 63 0.30
156 102 0.48
157 22 0.10
ACGTcount: A:0.13, C:0.36, G:0.33, T:0.18
Consensus pattern (155 bp):
CCGAGACACCCGTCGGGGTTGCCGATGGTGACCGAGACACCGTCTGGCTTTGCCAATGGTGACCG
AGGCACCCGTCTGGGATTGCCGATGGTGACCGAGACCCCGCACCCAACGCTCGGCTCTGTCCGCA
CTCCCGCACCCGTGGCCTGGGGTTG
Found at i:1867 original size:92 final size:93
Alignment explanation
Indices: 1504--1885 Score: 287
Period size: 92 Copynumber: 4.1 Consensus size: 93
1494 GCGAGGCTGC
* ** *
1504 CGCACCCAGCGCTCGGTTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTTGCCGAGGCACCC
1 CGCACCCAACGCTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGG-TTGCCGAGGCACCC
* *
1569 GTCGGTGTTGCCGATGGTGACCGAGGCCCC
65 GTCGGGGTTGCCGATGGTGACCGA-GCCCA
* *
1599 CGCACCCAACTCTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCT-GGGTTGCCGAGGCACCCG
1 CGCACCCAACGCTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCG
1663 TC-GGGTTGCCGATGGTGACCGAG---A
66 TCGGGGTTGCCGATGGTGACCGAGCCCA
* * ** * *
1687 --CA-CC--CGTCTGGGTTTGCCGATG-GTG-AC-CGAG-ACACCGTCTGGCTTTGCCAATGG-T
1 CGCACCCAACG-CTCGG-TT-CTG-TGCG-GCACTCCCGCAC-CCG--TGGC-CTG----GGGTT
* * *
1742 GACCGAGGCCACCCGCCTGTGATTGCCGATGGTGACCGAGCCTCA
53 G-CCGAGG-CACCCGTC-GGGGTTGCCGATGGTGACCGAGCC-CA
1787 CGCA-CCAACGCTCGGTTCTGTGC-GCACTCCCGCACCCGTGGCCTGGGGTTGCCGA-GCACCCG
1 CGCACCCAACGCTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCG
*
1849 TCGGGGGTTGCCGATGGTGACCGAGGCCCC
66 TC-GGGGTTGCCGATGGTGACCGA-GCCCA
1879 CGCACCC
1 CGCACCC
1886 CCGGCCTGGG
Statistics
Matches: 224, Mismatches: 30, Indels: 68
0.70 0.09 0.21
Matches are distributed among these distances:
83 1 0.00
84 6 0.03
85 8 0.04
86 7 0.03
87 7 0.03
88 1 0.00
91 1 0.00
92 52 0.23
93 31 0.14
94 16 0.07
95 42 0.19
96 19 0.08
98 2 0.01
99 5 0.02
100 5 0.02
101 7 0.03
102 8 0.04
103 4 0.02
104 2 0.01
ACGTcount: A:0.13, C:0.36, G:0.33, T:0.18
Consensus pattern (93 bp):
CGCACCCAACGCTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCG
TCGGGGTTGCCGATGGTGACCGAGCCCA
Found at i:1892 original size:62 final size:63
Alignment explanation
Indices: 1815--1948 Score: 234
Period size: 63 Copynumber: 2.1 Consensus size: 63
1805 TGTGCGCACT
** *
1815 CCCGCACCCGTGGCCTGGGGTTGCCGA-GCACCCGTCGGGGGTTGCCGATGGTGACCGAGGCC
1 CCCGCACCCCCGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGAC
1877 CCCGCACCCCCGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGAC
1 CCCGCACCCCCGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGAC
1940 CCCGCACCC
1 CCCGCACCC
1949 AACTCTCGGC
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
62 25 0.37
63 43 0.63
ACGTcount: A:0.10, C:0.39, G:0.38, T:0.13
Consensus pattern (63 bp):
CCCGCACCCCCGGCCTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGAC
Found at i:1931 original size:188 final size:186
Alignment explanation
Indices: 1558--1941 Score: 451
Period size: 188 Copynumber: 2.1 Consensus size: 186
1548 CTGGGGTTTG
* * *
1558 CCGAGGCACCCGTCGGTGTTGCCGATGGTGACCGAGGCCCCCGCACCCAACTCTCGGCTCTGTGC
1 CCGAGGCACCCGCCGGTGTTGCCGATGGTGACCGAGGCCCACGCACCCAACGCTCGGCTCTGTGC
1623 GGCACTCCCGCACCCGTGGCCTGGGTTGCCGAGGCACCCGTCGGGTTGCCGATGGTGACCGAGAC
66 GGCACTCCCGCACCCGTGGCCTGGGTTGCCGAGGCACCCGTCGGGTTGCCGATGGTGACCGAGAC
******* * * *
1688 ACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCGTCTGGCTTTGCCAATGGTGA
131 ACCCGTCACCCCCGGCCGAGGGTGACCGAGACACCGTCGGGCGTTGCCAATGGTGA
* *
1744 CCGAGGCCACCCGCCTGTGATTGCCGATGGTGACCGA-GCCTCACGCA-CCAACGCTCGGTTCTG
1 CCGAGG-CACCCGCCGGTG-TTGCCGATGGTGACCGAGGCC-CACGCACCCAACGCTCGGCTCTG
1807 TGC-GCACTCCCGCACCCGTGGCCTGGGGTTGCCGA-GCACCCGTCGGGGGTTGCCGATGGTGAC
63 TGCGGCACTCCCGCACCCGTGGCCT-GGGTTGCCGAGGCACCCGTC--GGGTTGCCGATGGTGAC
* * * * *
1870 CGAGGCCCCCG-CACCCCCGGCCTG-GGGTTG-CCGAGGCACCCGTCGGGGGTTGCCGATGGTGA
125 CGAGACACCCGTCACCCCCGGCC-GAGGG-TGACCGAGACA-CCGTCGGGCGTTGCCAATGGTGA
1932 CCGAGG-ACCC
1 CCGAGGCACCC
1942 CGCACCCAAC
Statistics
Matches: 169, Mismatches: 20, Indels: 18
0.82 0.10 0.09
Matches are distributed among these distances:
186 40 0.24
187 53 0.31
188 76 0.45
ACGTcount: A:0.13, C:0.36, G:0.34, T:0.17
Consensus pattern (186 bp):
CCGAGGCACCCGCCGGTGTTGCCGATGGTGACCGAGGCCCACGCACCCAACGCTCGGCTCTGTGC
GGCACTCCCGCACCCGTGGCCTGGGTTGCCGAGGCACCCGTCGGGTTGCCGATGGTGACCGAGAC
ACCCGTCACCCCCGGCCGAGGGTGACCGAGACACCGTCGGGCGTTGCCAATGGTGA
Found at i:2063 original size:33 final size:33
Alignment explanation
Indices: 1994--2114 Score: 130
Period size: 33 Copynumber: 3.8 Consensus size: 33
1984 CCTGGGGTTG
* *
1994 CCGAGCCACCCGTC-GGGGTTGCCGA---TGA-
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
*
2022 CCGAGACACCCGTCTGGTTTTGCCGATGGTGAC
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
2055 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA-
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
* * *
2087 CCGAGGCCCCCCGCCTGGG-TTGCCGATG
1 CCGA-GACACCCGTCTGGGTTTGCCGATG
2115 ACCGAGCCTC
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
28 13 0.16
29 9 0.11
32 16 0.20
33 42 0.52
ACGTcount: A:0.13, C:0.34, G:0.34, T:0.19
Consensus pattern (33 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGAC
Found at i:2238 original size:343 final size:334
Alignment explanation
Indices: 1548--2182 Score: 981
Period size: 343 Copynumber: 1.9 Consensus size: 334
1538 CACCAATGGA
* *
1548 CTGGGGTTTGCCGAGGCACCCGTCGGTGTTGCCGATGGTGACCGAGGCCCCCGCACCCAACTCTC
1 CTGGGG-TTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGACCCCGCACCCAACTCTC
* *
1613 GGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGTTGCCGAGGCACCCGTCGGGTTGCCGATGG
65 GGCTCTGTCCGGCACTCCCGCACCCGTGGCCTGGGTTGCCGAGCCACCCGTCGGGTTGCCGA--G
1678 TGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCGTCTGGCTTTGCCAATGGTG
128 TGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCGTCTGGCTTTGCCAATGGTG
1743 ACCGAGGCCACCCGCCTGTGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCTGT
193 ACCGAGGCCACCCGCCTGTGATTGCCGA--GTGACCGAGCCTCACGCACCAACGCTCGGTTCTGT
** *
1808 GCGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCACCCGTCGGGGGTTGCCGATGGTGACCGA
256 GCGCACTCCCGCACCAATGGCCTGGGGTTGCCGAGCACCCGTAGGGGGTTGCCGATGGTGACCGA
1873 GGCCCCCGCACCCCCGGC
321 GG---CCGCA-CCCCGGC
1891 CTGGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGACCCCGCACCCAACTCTC
1 CTGGGGTTGCCGAGGCACCCGTC-GGGGTTGCCGATGGTGACCGAGGACCCCGCACCCAACTCTC
1956 GGCTCTGTCCGG-ACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCGTCGGGGTTGCCGA-
65 GGCTCTGTCCGGCACTCCCGCACCCGTGGCCT-GGGTTGCCGAGCCACCCGTC-GGGTTGCCGAG
* * *
2019 TGACCGAGACACCCGTCTGGTTTTGCCGATGGTGACCCGAGACACCCGTCTGGGTTTGCCGATGG
128 TGACCGAGACACCCGTCTGGGTTTGCCGATGGTGA-CCGAGACA-CCGTCTGGCTTTGCCAATGG
* *
2084 TGACCGAGGCCCCCCGCCTG-GGTTGCCGA-TGACCGAGCCTCACGCACCAACGCTCGGTTTCTG
191 TGACCGAGGCCACCCGCCTGTGATTGCCGAGTGACCGAGCCTCACGCACCAACGCTCGG-TTCTG
*
2147 TGCGGCACTCCCTCACCAATGGCCTGGGGTTGCCGA
255 TGC-GCACTCCCGCACCAATGGCCTGGGGTTGCCGA
2183 TGGTGACCGA
Statistics
Matches: 273, Mismatches: 12, Indels: 16
0.91 0.04 0.05
Matches are distributed among these distances:
339 28 0.10
340 8 0.03
341 63 0.23
342 52 0.19
343 112 0.41
344 10 0.04
ACGTcount: A:0.13, C:0.36, G:0.33, T:0.18
Consensus pattern (334 bp):
CTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGACCCCGCACCCAACTCTCG
GCTCTGTCCGGCACTCCCGCACCCGTGGCCTGGGTTGCCGAGCCACCCGTCGGGTTGCCGAGTGA
CCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGACACCGTCTGGCTTTGCCAATGGTGACC
GAGGCCACCCGCCTGTGATTGCCGAGTGACCGAGCCTCACGCACCAACGCTCGGTTCTGTGCGCA
CTCCCGCACCAATGGCCTGGGGTTGCCGAGCACCCGTAGGGGGTTGCCGATGGTGACCGAGGCCG
CACCCCGGC
Found at i:2249 original size:33 final size:31
Alignment explanation
Indices: 2168--2255 Score: 104
Period size: 33 Copynumber: 2.8 Consensus size: 31
2158 CTCACCAATG
*
2168 GCCTGGGGTTGCCGATGGTGACCGAGACCCC
1 GCCTGGGATTGCCGATGGTGACCGAGACCCC
** ** *
2199 GTATGGTTTTGCCGATGGTGACCGAGGCCACCC
1 GCCTGGGATTGCCGATGGTGACCGA-GAC-CCC
2232 GCCTGGGATTGCCGATGGTGACCG
1 GCCTGGGATTGCCGATGGTGACCG
2256 GGGCTCACGC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
31 21 0.46
32 2 0.04
33 23 0.50
ACGTcount: A:0.14, C:0.28, G:0.38, T:0.20
Consensus pattern (31 bp):
GCCTGGGATTGCCGATGGTGACCGAGACCCC
Found at i:10508 original size:32 final size:32
Alignment explanation
Indices: 10472--10605 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
10462 CCTGGGGTTG
* * *
10472 CCGAGGCACCCGTCGGGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
10504 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
10536 CCGAGACACCCGTCTGGCTTTGCCAATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* * *
10568 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
10601 CCGAG
1 CCGAG
10606 CCTCACGCAC
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
32 64 0.70
33 27 0.30
ACGTcount: A:0.16, C:0.31, G:0.36, T:0.18
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Found at i:10699 original size:31 final size:31
Alignment explanation
Indices: 10664--10766 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
10654 CTGGGGTTTG
10664 CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
1 CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
* *** * *
10695 CCGAGGCCCCCG-CACCCGTGGCCTG-GGGTTG-
1 CCGAGGCACCCGTC-GGGGTTGCC-GATGG-TGA
10726 CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
1 CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
10757 CCGAGG-ACCC
1 CCGAGGCACCC
10767 CGCACCCAAC
Statistics
Matches: 54, Mismatches: 12, Indels: 13
0.68 0.15 0.16
Matches are distributed among these distances:
30 8 0.15
31 42 0.78
32 4 0.07
ACGTcount: A:0.12, C:0.35, G:0.40, T:0.14
Consensus pattern (31 bp):
CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
Found at i:10744 original size:62 final size:63
Alignment explanation
Indices: 10640--10773 Score: 252
Period size: 62 Copynumber: 2.1 Consensus size: 63
10630 GTGCGGCACT
*
10640 CCCGCACCCGTGGCCTGGGGTTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGCC
1 CCCGCACCCGTGGCCTGGGGTTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
10703 CCCGCACCCGTGGCCTGGGG-TTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
1 CCCGCACCCGTGGCCTGGGGTTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
10765 CCCGCACCC
1 CCCGCACCC
10774 AACTCTCGGC
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
62 50 0.71
63 20 0.29
ACGTcount: A:0.10, C:0.37, G:0.38, T:0.14
Consensus pattern (63 bp):
CCCGCACCCGTGGCCTGGGGTTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
Found at i:10771 original size:156 final size:157
Alignment explanation
Indices: 10568--10853 Score: 438
Period size: 156 Copynumber: 1.8 Consensus size: 157
10558 CCAATGGTGA
*
10568 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCA-CCAACGCTCGGTTCTGT
1 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCCAACGCTCGGCTCTGT
* * *
10632 GCGGCACTCCCGCACCCGTGGCCTGGGGTTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACC
66 CCGGAACTCCCGCACCCGTGGCCTGGGG-TTGCCGAGCCACCCGTCGGGGTTGCCGAT-GTGACC
10697 GAGGCCCCCGCACCCGTGGCCTGGGGTTG
129 GAGGCCCCCGCACCCGTGGCCTGGGGTTG
* * *
10726 CCGAGG-CACCCGTC-GGGGTTGCCGATGGTGACCGAGGACC-C-CGCACCCAACTCTCGGCTCT
1 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGA-G-CCTCACGCACCCAACGCTCGGCTCT
10787 GTCCGGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCGTCGGGGTTGCCGATGTGACC
64 GTCCGGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCGTCGGGGTTGCCGATGTGACC
10852 GA
129 GA
10854 CACCCGTCTG
Statistics
Matches: 118, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
155 8 0.07
156 52 0.44
157 50 0.42
158 8 0.07
ACGTcount: A:0.12, C:0.37, G:0.35, T:0.16
Consensus pattern (157 bp):
CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCCAACGCTCGGCTCTGT
CCGGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCGTCGGGGTTGCCGATGTGACCGA
GGCCCCCGCACCCGTGGCCTGGGGTTG
Found at i:10882 original size:30 final size:29
Alignment explanation
Indices: 10826--10946 Score: 131
Period size: 33 Copynumber: 4.0 Consensus size: 29
10816 GTTGCCGAGC
*
10826 CACCCGTC-GGGGTTGCCGATGTGACCGA
1 CACCCGTCTGGGTTTGCCGATGTGACCGA
10854 CACCCGTCTGGGTTTGCCGATGGTGACCGAGA
1 CACCCGTCTGGGTTTGCCGAT-GTGACC--GA
10886 CACCCCGTCTGGGTTTGCCGATG-GACCGA
1 CA-CCCGTCTGGGTTTGCCGATGTGACCGA
*
10915 GGCCACCCGCCTGGG-TTGCCGATGGTGACCGA
1 ---CACCCGTCTGGGTTTGCCGAT-GTGACCGA
10947 GCCTCACGCA
Statistics
Matches: 81, Mismatches: 2, Indels: 16
0.82 0.02 0.16
Matches are distributed among these distances:
28 8 0.10
29 13 0.16
30 14 0.17
31 14 0.17
32 13 0.16
33 19 0.23
ACGTcount: A:0.14, C:0.32, G:0.35, T:0.19
Consensus pattern (29 bp):
CACCCGTCTGGGTTTGCCGATGTGACCGA
Found at i:10946 original size:63 final size:60
Alignment explanation
Indices: 10820--10947 Score: 170
Period size: 63 Copynumber: 2.1 Consensus size: 60
10810 CCTGGGGTTG
* *
10820 CCGAGCCACCCGTCGGGGTTGCCGATGTGACCGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCGGGGTTGCCGATGTGACCGACACCCGCCTGGGTTTGCCGATGGTGA
*
10880 CCGAGACACCCCGTCTGGGTTTGCCGATG-GACCGAGGCCACCCGCCTGGG-TTGCCGATGGTGA
1 CCGAGACA-CCCGTC-GGGGTTGCCGATGTGACCGA---CACCCGCCTGGGTTTGCCGATGGTGA
10943 CCGAG
1 CCGAG
10948 CCTCACGCAC
Statistics
Matches: 60, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
60 7 0.12
61 12 0.20
62 12 0.20
63 18 0.30
64 11 0.18
ACGTcount: A:0.14, C:0.33, G:0.35, T:0.18
Consensus pattern (60 bp):
CCGAGACACCCGTCGGGGTTGCCGATGTGACCGACACCCGCCTGGGTTTGCCGATGGTGA
Found at i:11074 original size:33 final size:31
Alignment explanation
Indices: 10994--11080 Score: 120
Period size: 31 Copynumber: 2.7 Consensus size: 31
10984 CTCACCAATG
10994 GCCTGGGTTGCCGATGGTGACCGAGACACCC
1 GCCTGGGTTGCCGATGGTGACCGAGACACCC
** * *
11025 GTATGGTTTGCCGATGGTGACCGAGGCCACCC
1 GCCTGGGTTGCCGATGGTGACCGA-GACACCC
11057 GCCTGGGATTGCCGATGGTGACCG
1 GCCTGGG-TTGCCGATGGTGACCG
11081 GGCTCACGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 21 0.45
32 10 0.21
33 16 0.34
ACGTcount: A:0.15, C:0.29, G:0.37, T:0.20
Consensus pattern (31 bp):
GCCTGGGTTGCCGATGGTGACCGAGACACCC
Found at i:19311 original size:96 final size:96
Alignment explanation
Indices: 19147--19325 Score: 295
Period size: 96 Copynumber: 1.9 Consensus size: 96
19137 TGCGAGGCTG
* *
19147 CCGCACCCAGCGCTCGGTTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
1 CCGCACCCAACGCTCGGCTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
*
19212 GTCGGGTGTTGCCGATGGTGACCGAGGCCCC
66 GTCGGGGGTTGCCGATGGTGACCGAGGCCCC
* ** *
19243 CCGCACCCAACTCTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC
1 CCGCACCCAACGCTCGGCTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
19308 GTCGGGGGTTGCCGATGG
66 GTCGGGGGTTGCCGATGG
19326 ACCGAGACAC
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 76 1.00
ACGTcount: A:0.11, C:0.37, G:0.35, T:0.17
Consensus pattern (96 bp):
CCGCACCCAACGCTCGGCTCTGTGCGGCACTCCCGCACCAATGGACTGGGGTTGCCGAGGCACCC
GTCGGGGGTTGCCGATGGTGACCGAGGCCCC
Found at i:19415 original size:33 final size:32
Alignment explanation
Indices: 19297--19428 Score: 169
Period size: 32 Copynumber: 4.2 Consensus size: 32
19287 CCTGGGGTTG
* * *
19297 CCGAGGCACCCGTCGGGGGTTGCCGAT-G-GA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
19327 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
19359 CCGAGACACCCGTCTGGCTTTGCCAATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* * *
19391 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
19424 CCGAG
1 CCGAG
19429 CCTCACGCAC
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
30 24 0.27
31 1 0.01
32 37 0.42
33 27 0.30
ACGTcount: A:0.16, C:0.31, G:0.36, T:0.17
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Found at i:19574 original size:62 final size:59
Alignment explanation
Indices: 19463--19592 Score: 215
Period size: 62 Copynumber: 2.2 Consensus size: 59
19453 GTGCGGCACT
* *
19463 CCCGCACCCGTGGCCTGGGTTTGCCGCACCCGTCGGGGTTGCCGATGGTGACCGAGGCC
1 CCCGCACCCGTGGCCTGGGGTTGCCGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
19522 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
1 CCCGCACCCGTGGCCTGGGGTTGCC---GCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
19584 CCCGCACCC
1 CCCGCACCC
19593 AACTCTCGGC
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
59 24 0.36
62 42 0.64
ACGTcount: A:0.10, C:0.38, G:0.37, T:0.15
Consensus pattern (59 bp):
CCCGCACCCGTGGCCTGGGGTTGCCGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
Found at i:19580 original size:31 final size:31
Alignment explanation
Indices: 19488--19585 Score: 87
Period size: 31 Copynumber: 3.2 Consensus size: 31
19478 TGGGTTTGCC
19488 GCACCCGTCGGGGTTGCCGATGGTGACCGAG
1 GCACCCGTCGGGGTTGCCGATGGTGACCGAG
* *** * *
19519 GCCCCCG-CACCCGTGGCCTG-GGGTTG-CCGAG
1 GCACCCGTC-GGGGTTGCC-GATGG-TGACCGAG
19550 GCACCCGTCGGGGTTGCCGATGGTGACCGAG
1 GCACCCGTCGGGGTTGCCGATGGTGACCGAG
19581 G-ACCC
1 GCACCC
19586 CGCACCCAAC
Statistics
Matches: 49, Mismatches: 12, Indels: 13
0.66 0.16 0.18
Matches are distributed among these distances:
30 8 0.16
31 37 0.76
32 4 0.08
ACGTcount: A:0.11, C:0.35, G:0.40, T:0.14
Consensus pattern (31 bp):
GCACCCGTCGGGGTTGCCGATGGTGACCGAG
Found at i:19617 original size:153 final size:156
Alignment explanation
Indices: 19391--19674 Score: 427
Period size: 153 Copynumber: 1.8 Consensus size: 156
19381 CCAATGGTGA
* *
19391 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGTTCTGTG
1 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGCTCTGTC
* *
19456 CGGCACTCCCGCACCCGTGGCCTGGGTTTGCC-G-CACCCGTCGGGGTTGCCGATGGTGACCGAG
66 CGGAACTCCCGCACCCGTGGCCTGGGGTTGCCAGCCACCCGTCGGGGTTGCCGATGGTGACCGAG
19519 GCCCCCGCACCCGTGGCCTGGGGTTG
131 GCCCCCGCACCCGTGGCCTGGGGTTG
* * *
19545 CCGAGG-CACCCGTC-GGGGTTGCCGATGGTGACCGAGGACC-C-CGCACCCAACTCTCGGCTCT
1 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGA-G-CCTCACGCA-CCAACGCTCGGCTCT
19606 GTCCGGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCGTCGGGGTTGCCGATGGTGAC
63 GTCCGGAACTCCCGCACCCGTGGCCTGGGGTTGCC-AGCCACCCGTCGGGGTTGCCGATGGTGAC
19671 CGAG
127 CGAG
19675 ACACCCGTCT
Statistics
Matches: 117, Mismatches: 7, Indels: 10
0.87 0.05 0.07
Matches are distributed among these distances:
152 24 0.21
153 54 0.46
154 8 0.07
155 1 0.01
156 30 0.26
ACGTcount: A:0.12, C:0.37, G:0.35, T:0.16
Consensus pattern (156 bp):
CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGCCTCACGCACCAACGCTCGGCTCTGTC
CGGAACTCCCGCACCCGTGGCCTGGGGTTGCCAGCCACCCGTCGGGGTTGCCGATGGTGACCGAG
GCCCCCGCACCCGTGGCCTGGGGTTG
Found at i:19698 original size:32 final size:32
Alignment explanation
Indices: 19639--19769 Score: 191
Period size: 32 Copynumber: 4.2 Consensus size: 32
19629 CCTGGGGTTG
*
19639 CCGAGCCACCCGTC-GGGGTTGCCGATGGTGA
1 CCGAGCCACCCGTCTGGGTTTGCCGATGGTGA
*
19670 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGCCACCCGTCTGGGTTTGCCGATGGTGA
19702 CCGAG--ACCCGTCT-GGTTTGCCGATGGTGA
1 CCGAGCCACCCGTCTGGGTTTGCCGATGGTGA
*
19731 CCGAGGCCACCCGCCTGGG-TTGCCGATGGTGA
1 CCGA-GCCACCCGTCTGGGTTTGCCGATGGTGA
19763 CCGAGCC
1 CCGAGCC
19770 TCACGCACCA
Statistics
Matches: 92, Mismatches: 3, Indels: 10
0.88 0.03 0.10
Matches are distributed among these distances:
29 20 0.22
30 9 0.10
31 16 0.17
32 45 0.49
33 2 0.02
ACGTcount: A:0.14, C:0.32, G:0.36, T:0.18
Consensus pattern (32 bp):
CCGAGCCACCCGTCTGGGTTTGCCGATGGTGA
Found at i:19723 original size:61 final size:61
Alignment explanation
Indices: 19646--19767 Score: 192
Period size: 61 Copynumber: 2.0 Consensus size: 61
19636 TTGCCGAGCC
*
19646 ACCCGTCGGGGTTGCCGATGGTGACCGA-GACACCCGTCTGGGTTTGCCGATGGTGACCGAG
1 ACCCGTCGGGGTTGCCGATGGTGACCGAGGACACCCGCCTGGG-TTGCCGATGGTGACCGAG
* * *
19707 ACCCGTCTGGTTTGCCGATGGTGACCGAGGCCACCCGCCTGGGTTGCCGATGGTGACCGAG
1 ACCCGTCGGGGTTGCCGATGGTGACCGAGGACACCCGCCTGGGTTGCCGATGGTGACCGAG
19768 CCTCACGCAC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
61 44 0.79
62 12 0.21
ACGTcount: A:0.14, C:0.30, G:0.37, T:0.20
Consensus pattern (61 bp):
ACCCGTCGGGGTTGCCGATGGTGACCGAGGACACCCGCCTGGGTTGCCGATGGTGACCGAG
Found at i:19890 original size:33 final size:31
Alignment explanation
Indices: 19814--19901 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 31
19804 CTCACCAATG
19814 GCCTGGGTTGCCGATGGTGACCGAGACACCC
1 GCCTGGGTTGCCGATGGTGACCGAGACACCC
** * *
19845 GTATGGTTTTGCCGATGGTGACCGAGGCCACCC
1 GCCTGG-GTTGCCGATGGTGACCGA-GACACCC
19878 GCCTGGGATTGCCGATGGTGACCG
1 GCCTGGG-TTGCCGATGGTGACCG
19902 GGGCTCACGC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 4 0.09
32 17 0.36
33 26 0.55
ACGTcount: A:0.15, C:0.28, G:0.36, T:0.20
Consensus pattern (31 bp):
GCCTGGGTTGCCGATGGTGACCGAGACACCC
Done.