Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009433.1 Hibiscus syriacus cultivar Beakdansim tig00113451_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: 23061
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.22
Found at i:1629 original size:95 final size:91
Alignment explanation
Indices: 1475--1656 Score: 274
Period size: 95 Copynumber: 2.0 Consensus size: 91
1465 TGCGAGGCTG
* * *
1475 CCGCACCCAGCGCTCGTTCTGTGCGGCACTCCGCACCATGGACTTGGGTTGCCGAGGCACCCGTC
1 CCGCACCCAACGCTCGCTCTGTGCGGCACTCCGCACCATGGACTGGGGTTGCCGAGGCACCCGTC
1540 GGGTGTTGCCGATGGTGACCGAGGCCC
66 GGG-GTTGCCGATGGTGACCGAGGCCC
* * *
1567 CCGCACCCAACTCTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC
1 CCGCACCCAACGCTC-GCTCTGTGCGGCACT-CCGCA-CCATGGACTGGGGTTGCCGAGGCACCC
1632 GTCGGGGTTGCCGATGGTGACCGAG
63 GTCGGGGTTGCCGATGGTGACCGAG
1657 ACACCCGTCT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
92 13 0.16
93 14 0.17
94 24 0.30
95 30 0.37
ACGTcount: A:0.12, C:0.37, G:0.34, T:0.18
Consensus pattern (91 bp):
CCGCACCCAACGCTCGCTCTGTGCGGCACTCCGCACCATGGACTGGGGTTGCCGAGGCACCCGTC
GGGGTTGCCGATGGTGACCGAGGCCC
Found at i:1680 original size:32 final size:32
Alignment explanation
Indices: 1621--1753 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
1611 CCTGGGGTTG
* *
1621 CCGAGGCACCCGTC-GGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1652 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
1684 CCGAGACACCCGTCTGGCTTTGCCAATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* * *
1716 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
1749 CCGAG
1 CCGAG
1754 CCTCACGCAC
Statistics
Matches: 91, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
31 13 0.14
32 51 0.56
33 27 0.30
ACGTcount: A:0.16, C:0.31, G:0.35, T:0.18
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Found at i:1741 original size:65 final size:63
Alignment explanation
Indices: 1621--1753 Score: 185
Period size: 65 Copynumber: 2.1 Consensus size: 63
1611 CCTGGGGTTG
* * * * *
1621 CCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCGGCGTTGCCAATGGTGACCGAGACACCCGCCTGGGATTGCCGATGGTGA
* *
1684 CCGAGACACCCGTCTGGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGAGACACCCGTC-GGCGTTGCCAATGGTGACCGA-GACACCCGCCTGGGATTGCCGATGGTGA
1749 CCGAG
1 CCGAG
1754 CCTCACGCAC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 13 0.21
64 18 0.30
65 30 0.49
ACGTcount: A:0.16, C:0.31, G:0.35, T:0.18
Consensus pattern (63 bp):
CCGAGACACCCGTCGGCGTTGCCAATGGTGACCGAGACACCCGCCTGGGATTGCCGATGGTGA
Found at i:1900 original size:63 final size:59
Alignment explanation
Indices: 1788--1917 Score: 199
Period size: 63 Copynumber: 2.2 Consensus size: 59
1778 GTGCGGCACT
*
1788 CCCGCA-CCGTGGCCTGGGTTGCCGAGGCCCGTCGGGGTTGCCGATGGTGACCGAGGCC
1 CCCGCACCCGTGGCCTGGGTTGCCGAGGCCCGTCGGGGTTGCCGATGGTGACCGAGGAC
*
1846 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCTGGGTTTGCCGATGGTGACCGAGGAC
1 CCCGCACCCGTGGCCT-GGGTTGCCGAGG--CCCGTC-GGGGTTGCCGATGGTGACCGAGGAC
1909 CCCGCACCC
1 CCCGCACCC
1918 AACTCTCGGC
Statistics
Matches: 65, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
58 6 0.09
59 9 0.14
60 12 0.18
62 6 0.09
63 32 0.49
ACGTcount: A:0.10, C:0.37, G:0.38, T:0.15
Consensus pattern (59 bp):
CCCGCACCCGTGGCCTGGGTTGCCGAGGCCCGTCGGGGTTGCCGATGGTGACCGAGGAC
Found at i:2006 original size:32 final size:31
Alignment explanation
Indices: 1960--2093 Score: 157
Period size: 32 Copynumber: 4.3 Consensus size: 31
1950 GTGGCCTGGG
*
1960 GGTG-CCGAGCCACCCGTCGGGGGTTGCCGAT
1 GGTGACCGAGACACCCGTC-GGGGTTGCCGAT
*
1991 GGTGACCGAGACACCCGTCTGGGTTTGCCGAT
1 GGTGACCGAGACACCCGTC-GGGGTTGCCGAT
* *
2023 GGTGACC--GACACCCGTCTGGTTTGCCGAT
1 GGTGACCGAGACACCCGTCGGGGTTGCCGAT
* * *
2052 GGTGACCGAGGCCACCCGCCTGGGTTGCCGAT
1 GGTGACCGA-GACACCCGTCGGGGTTGCCGAT
2084 GGTGACCGAG
1 GGTGACCGAG
2094 CCTCACGCAA
Statistics
Matches: 92, Mismatches: 7, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.20
30 10 0.11
31 5 0.05
32 59 0.64
ACGTcount: A:0.13, C:0.31, G:0.37, T:0.19
Consensus pattern (31 bp):
GGTGACCGAGACACCCGTCGGGGTTGCCGAT
Found at i:2085 original size:188 final size:194
Alignment explanation
Indices: 1869--2228 Score: 441
Period size: 188 Copynumber: 1.9 Consensus size: 194
1859 CCTGGGGTTG
* * *
1869 CCGAGGCACCCGTCTGGGTTTGCCGATGGTGACCGAGGACC-C-CGCACCCAACTCTCGGCTCTG
1 CCGAGGCACCCGCCTGGGTTTGCCGATGGTGACCGA-G-CCTCACGCAACCAACGCTCGGCTCTG
** * *
1932 TCCGGAACTCCCGCACCCGTGGCCT-G-G-G-GGTG-CCGAGCCACCCGTCGGGGGTTGCCGATG
64 TCCGGAACTCCCGCACCAATGGCCTGGTGCGAGGTGACCGAGACACCCGTAGGGGGTTGCCGATG
* *
1992 GTGACCGA-GACACCCGTCTGGGTTTGCCGATGGTGACCGACACCCGTCTGGTTTGCCGATGGTG
129 GTGACCGAGGACACCCGCCTGGGATTGCCGATGGTGACCGACACCCGTCTGGTTTGCCGATGGTG
2056 A
194 A
*
2057 CCGAGGCCACCCGCCTGGG-TTGCCGATGGTGACCGAGCCTCACGCAACCAACGCTCGGTTCTGT
1 CCGAGG-CACCCGCCTGGGTTTGCCGATGGTGACCGAGCCTCACGCAACCAACGCTCGGCTCTGT
* * * * **
2121 GCGGCACTCCCTCACCAATGGCCTGGGTTGCCGATGGTGACCGAGACACCCGTATGGTTTTGCCG
65 CCGGAACTCCCGCACCAATGGCCT-GG-TG-CGA-GGTGACCGAGACACCCGTAGGGGGTTGCCG
*
2186 ATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCG
126 ATGGTGACCGAGGACACCCGCCTGGGATTGCCGATGGTGACCG
2229 GGCTCACGCA
Statistics
Matches: 142, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
186 2 0.01
187 2 0.01
188 61 0.43
189 11 0.08
190 1 0.01
192 1 0.01
194 1 0.01
196 4 0.03
197 31 0.22
198 28 0.20
ACGTcount: A:0.14, C:0.34, G:0.33, T:0.19
Consensus pattern (194 bp):
CCGAGGCACCCGCCTGGGTTTGCCGATGGTGACCGAGCCTCACGCAACCAACGCTCGGCTCTGTC
CGGAACTCCCGCACCAATGGCCTGGTGCGAGGTGACCGAGACACCCGTAGGGGGTTGCCGATGGT
GACCGAGGACACCCGCCTGGGATTGCCGATGGTGACCGACACCCGTCTGGTTTGCCGATGGTGA
Found at i:2217 original size:33 final size:31
Alignment explanation
Indices: 2141--2228 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 31
2131 CTCACCAATG
2141 GCCTGGGTTGCCGATGGTGACCGAGACACCC
1 GCCTGGGTTGCCGATGGTGACCGAGACACCC
** * *
2172 GTATGGTTTTGCCGATGGTGACCGAGGCCACCC
1 GCCTGG-GTTGCCGATGGTGACCGA-GACACCC
2205 GCCTGGGATTGCCGATGGTGACCG
1 GCCTGGG-TTGCCGATGGTGACCG
2229 GGCTCACGCA
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
Found at i:10497 original size:32 final size:32
Alignment explanation
Indices: 10461--10593 Score: 178
Period size: 32 Copynumber: 4.2 Consensus size: 32
10451 CCTGGGGTTG
* *
10461 CCGAGGCACCCGTCGGGGGTTGCCGATGGTGA
1 CCGAGGCACCCGTCTGGGTTTGCCGATGGTGA
*
10493 CCGA-GAACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGGCACCCGTCTGGGTTTGCCGATGGTGA
* * *
10524 CCGAGACACCCGTCTGGCTTTGCCAATGGTGA
1 CCGAGGCACCCGTCTGGGTTTGCCGATGGTGA
* *
10556 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGAGG-CACCCGTCTGGGTTTGCCGATGGTGA
10589 CCGAG
1 CCGAG
10594 CCTCACGCAC
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
31 28 0.32
32 32 0.37
33 27 0.31
ACGTcount: A:0.16, C:0.30, G:0.36, T:0.18
Consensus pattern (32 bp):
CCGAGGCACCCGTCTGGGTTTGCCGATGGTGA
Found at i:10503 original size:31 final size:31
Alignment explanation
Indices: 10468--10593 Score: 162
Period size: 31 Copynumber: 4.0 Consensus size: 31
10458 TTGCCGAGGC
* *
10468 ACCCGTCGGGGGTTGCCGATGGTGACCGAGA
1 ACCCGTCTGGGTTTGCCGATGGTGACCGAGA
10499 ACCCGTCTGGGTTTGCCGATGGTGACCGAGA
1 ACCCGTCTGGGTTTGCCGATGGTGACCGAGA
* * *
10530 CACCCGTCTGGCTTTGCCAATGGTGACCGAGGCC
1 -ACCCGTCTGGGTTTGCCGATGGTGACCGA-G-A
* *
10564 ACCCGCCTGGGATTGCCGATGGTGACCGAG
1 ACCCGTCTGGGTTTGCCGATGGTGACCGAG
10594 CCTCACGCAC
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
31 29 0.35
32 28 0.34
33 26 0.31
ACGTcount: A:0.16, C:0.29, G:0.36, T:0.19
Consensus pattern (31 bp):
ACCCGTCTGGGTTTGCCGATGGTGACCGAGA
Found at i:10560 original size:63 final size:65
Alignment explanation
Indices: 10461--10593 Score: 180
Period size: 63 Copynumber: 2.1 Consensus size: 65
10451 CCTGGGGTTG
* * * * *
10461 CCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGA-G-AACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCGGGCGTTGCCAATGGTGACCGAGGCAACCCGCCTGGGATTGCCGATGGTGA
* * *
10524 CCGAGACACCCGTCTGGCTTTGCCAATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGAGACACCCGTCGGGCGTTGCCAATGGTGACCGAGGCAACCCGCCTGGGATTGCCGATGGTGA
10589 CCGAG
1 CCGAG
10594 CCTCACGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
63 31 0.52
64 1 0.02
65 28 0.47
ACGTcount: A:0.16, C:0.30, G:0.36, T:0.18
Consensus pattern (65 bp):
CCGAGACACCCGTCGGGCGTTGCCAATGGTGACCGAGGCAACCCGCCTGGGATTGCCGATGGTGA
Found at i:10701 original size:60 final size:61
Alignment explanation
Indices: 10628--10757 Score: 228
Period size: 62 Copynumber: 2.1 Consensus size: 61
10618 GTGCGGCACT
*
10628 CCCGCA-CCGTGGCCTGGGGTTGCCGAGGCACCCG-GGGGTTGCCGATGGTGACCGAGGCC
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGCGGGGTTGCCGATGGTGACCGAGGAC
10687 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGAC
1 CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCG-CGGGGTTGCCGATGGTGACCGAGGAC
10749 CCCGCACCC
1 CCCGCACCC
10758 ACTCTCGGCT
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
59 6 0.09
60 28 0.42
62 33 0.49
ACGTcount: A:0.11, C:0.37, G:0.39, T:0.13
Consensus pattern (61 bp):
CCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGCGGGGTTGCCGATGGTGACCGAGGAC
Found at i:10745 original size:31 final size:30
Alignment explanation
Indices: 10650--10750 Score: 84
Period size: 31 Copynumber: 3.4 Consensus size: 30
10640 CCTGGGGTTG
10650 CCGAGGCACCCG-GGGGTTGCCGATGGTGA
1 CCGAGGCACCCGCGGGGTTGCCGATGGTGA
* *** * *
10679 CCGAGGCCCCCGCACCCGTGGCCTG-GGGTTG-
1 CCGAGGCACCCGC-GGGGTTGCC-GATGG-TGA
10710 CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
1 CCGAGGCACCCG-CGGGGTTGCCGATGGTGA
10741 CCGAGG-ACCC
1 CCGAGGCACCC
10751 CGCACCCACT
Statistics
Matches: 53, Mismatches: 12, Indels: 13
0.68 0.15 0.17
Matches are distributed among these distances:
29 11 0.21
30 7 0.13
31 31 0.58
32 4 0.08
ACGTcount: A:0.12, C:0.35, G:0.41, T:0.13
Consensus pattern (30 bp):
CCGAGGCACCCGCGGGGTTGCCGATGGTGA
Found at i:10745 original size:152 final size:156
Alignment explanation
Indices: 10556--10834 Score: 401
Period size: 152 Copynumber: 1.8 Consensus size: 156
10546 CCAATGGTGA
*
10556 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGA-G-CCTCACGCACCAACGCTCGGTTCTG
1 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGGACC-C-CGCACCAACGCTCGGCTCTG
* * *
10619 TGCGGCACTCCCGCA-CCGTGGCCTGGGGTTGCCGAGGCA-CC-CGGGGGTTGCCGATGGTGACC
64 T-CCGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCGCGGGGGTTGCCGATGGTGACC
10681 GAGGCCCCCGCACCCGTGGCCTGGGGTTG
128 GAGGCCCCCGCACCCGTGGCCTGGGGTTG
* * * *
10710 CCGAGG-CACCCGTC-GGGGTTGCCGATGGTGACCGAGGACCCCGCACCCACTCTCGGCTCTGTC
1 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGGACCCCGCACCAACGCTCGGCTCTGTC
10773 CGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCGTCGGGGGTTGCCGATGGTGAC
66 CGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCG-CGGGGGTTGCCGATGGTGAC
10835 GAGACACCCG
Statistics
Matches: 111, Mismatches: 8, Indels: 11
0.85 0.06 0.08
Matches are distributed among these distances:
151 11 0.10
152 61 0.55
153 11 0.10
154 8 0.07
155 20 0.18
ACGTcount: A:0.12, C:0.37, G:0.35, T:0.16
Consensus pattern (156 bp):
CCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGGACCCCGCACCAACGCTCGGCTCTGTC
CGAACTCCCGCACCCGTGGCCTGGGGTTGCCGAGCCACCCGCGGGGGTTGCCGATGGTGACCGAG
GCCCCCGCACCCGTGGCCTGGGGTTG
Found at i:10917 original size:32 final size:31
Alignment explanation
Indices: 10802--10926 Score: 166
Period size: 30 Copynumber: 4.0 Consensus size: 31
10792 CCTGGGGTTG
* *
10802 CCGAGCCACCCGTCGGGGGTTGCCGATGGTGA
1 CCGAGACACCCGTC-TGGGTTGCCGATGGTGA
10834 -CGAGACACCCGTC-GGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGG-TTGCCGATGGTGA
10864 CCGAGACA-CCGTCTGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTGCCGATGGTGA
* *
10894 CCGAGGCCACCCGCCTGGGTTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTGCCGATGGTGA
10926 C
1 C
10927 GAGCCTCACG
Statistics
Matches: 85, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
29 3 0.04
30 35 0.41
31 25 0.29
32 22 0.26
ACGTcount: A:0.14, C:0.30, G:0.38, T:0.18
Consensus pattern (31 bp):
CCGAGACACCCGTCTGGGTTGCCGATGGTGA
Found at i:11022 original size:33 final size:33
Alignment explanation
Indices: 10975--11061 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 33
10965 CTCAATGGCC
* *
10975 TGGGGTTGCCGATGGTGACCGA-GACACCCGTA
1 TGGGATTGCCGATGGTGACCGAGGACACCCGCA
** * *
11007 TGGTTTTTGCCGATGGTGACCGAGGCCACCCGCC
1 TGG-GATTGCCGATGGTGACCGAGGACACCCGCA
11041 TGGGATTGCCGATGGTGACCG
1 TGGGATTGCCGATGGTGACCG
11062 GGCTCAGCAC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
32 3 0.07
33 33 0.72
34 10 0.22
ACGTcount: A:0.15, C:0.26, G:0.37, T:0.22
Consensus pattern (33 bp):
TGGGATTGCCGATGGTGACCGAGGACACCCGCA
Found at i:11077 original size:33 final size:33
Alignment explanation
Indices: 10974--11077 Score: 81
Period size: 33 Copynumber: 3.2 Consensus size: 33
10964 CCTCAATGGC
* * *
10974 CTGGGGTTGCCGATGGTGACCGA-GACACCCGTA
1 CTGGGATTGCCGATGGTGACCGAGGCCACACG-A
** * *
11007 -TGGTTTTTGCCGATGGTGACCGAGGCCACCCGC
1 CTGG-GATTGCCGATGGTGACCGAGGCCACACGA
11040 CTGGGATTGCCGATGGTGACCG-GGCTCAGCAC-A
1 CTGGGATTGCCGATGGTGACCGAGGC-CA-CACGA
11073 CTGGG
1 CTGGG
11078 GCCTGATGGT
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
32 6 0.10
33 40 0.69
34 12 0.21
ACGTcount: A:0.15, C:0.28, G:0.37, T:0.20
Consensus pattern (33 bp):
CTGGGATTGCCGATGGTGACCGAGGCCACACGA
Done.