Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007616.1 Hibiscus syriacus cultivar Beakdansim tig00022762_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: 26607
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Found at i:1490 original size:11 final size:11
Alignment explanation
Indices: 1474--1505 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1464 CGATAATGTC
1474 TCGCCGGAGCG
1 TCGCCGGAGCG
1485 TCGCCGGAGCG
1 TCGCCGGAGCG
1496 TCGCCGGAGC
1 TCGCCGGAGC
1506 ACCACCGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.38, G:0.44, T:0.09
Consensus pattern (11 bp):
TCGCCGGAGCG
Found at i:1958 original size:33 final size:32
Alignment explanation
Indices: 1895--2116 Score: 198
Period size: 32 Copynumber: 6.6 Consensus size: 32
1885 ATGGCCCGGG
* * *
1895 TTGCCGATGGTGACCGAGACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGGCACCCGCCTGGGA
1927 TTGCCGATGGTGACCGAGGCAACCCGCCTGGGA
1 TTGCCGATGGTGACCGAGGC-ACCCGCCTGGGA
* * * *
1960 CTGCCGATGGTGACCGAGGCTCACGCACAAGGG-
1 TTGCCGATGGTGACCGAGGCACCCGC-C-TGGGA
* *
1993 --GCCTGATGGTGACCGAGGCTCCCGCACCAATGGCCCGGG
1 TTGCC-GATGGTGACCGAGGCACCCG--CC--T-G---GGA
* * *
2032 TTGCCGATGGTGACCGAGACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGGCACCCGCCTGGGA
2064 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
1 TTGCCGATGGTGACCGAGG-CACCCGCCTGGGA
2097 TTGCCGATGGTGACCGAGGC
1 TTGCCGATGGTGACCGAGGC
2117 TCACGCACAA
Statistics
Matches: 159, Mismatches: 16, Indels: 30
0.78 0.08 0.15
Matches are distributed among these distances:
31 3 0.02
32 63 0.40
33 61 0.38
34 5 0.03
35 2 0.01
36 1 0.01
38 3 0.02
40 18 0.11
41 3 0.02
ACGTcount: A:0.17, C:0.31, G:0.36, T:0.17
Consensus pattern (32 bp):
TTGCCGATGGTGACCGAGGCACCCGCCTGGGA
Found at i:2057 original size:137 final size:136
Alignment explanation
Indices: 1877--2158 Score: 528
Period size: 137 Copynumber: 2.1 Consensus size: 136
1867 GGCGGCACTA
1877 CCGCACCAATGGCCCGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACC
1 CCGCACCAATGGCCCGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACC
1942 GAGGCAACCCGCCTGGGACTGCCGATGGTGACCGAGGCTCACGCACAAGGGGCCTGATGGTGACC
66 GAGGCAACCCGCCTGGGACTGCCGATGGTGACCGAGGCTCACGCACAAGGGGCCTGATGGT-ACC
*
2007 GAGGCTC
130 GAGACTC
2014 CCGCACCAATGGCCCGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACC
1 CCGCACCAATGGCCCGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACC
* *
2079 GAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGGCTCACGCACAAGGGGCCTGATGGTACCG
66 GAGGCAACCCGCCTGGGACTGCCGATGGTGACCGAGGCTCACGCACAAGGGGCCTGATGGTACCG
2144 AGACTC
131 AGACTC
2150 CCGCACCAA
1 CCGCACCAA
2159 CGCTCGGTTC
Statistics
Matches: 142, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
136 18 0.13
137 124 0.87
ACGTcount: A:0.18, C:0.32, G:0.34, T:0.15
Consensus pattern (136 bp):
CCGCACCAATGGCCCGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACC
GAGGCAACCCGCCTGGGACTGCCGATGGTGACCGAGGCTCACGCACAAGGGGCCTGATGGTACCG
AGACTC
Found at i:2184 original size:167 final size:169
Alignment explanation
Indices: 2011--2585 Score: 907
Period size: 167 Copynumber: 3.4 Consensus size: 169
2001 GTGACCGAGG
2011 CTCCCGCACCAATGGCCCGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTG
1 CTCCCGCACCAATGGCCCGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTG
* * *
2076 ACCGAGGCCACCCGCCTGGGATTGCCGATGGTGACCGAGGCTCACGCACA-AGGGGCCTGATGGT
66 ACCGAGGCCACCCGCCTAGGATTACCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGGT
*
2140 -ACCGAGACTCCCGCACCAACGCTCGGTTCTGTGCGGCA
131 GACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
2178 CTCCCGCACCAATGGCCCGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTG
1 CTCCCGCACCAATGGCCCGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTG
* * *
2243 -CCGAGGCCACCCGCCCAGGATTACCGATGGTGTGTCCGAGGCT-ACTCACACGGGGGCCTGATG
66 ACCGAGGCCACCCGCCTAGGATTACCGAT-G-GTGACCGAGGCTCACGCACACGGGGGCCTGATG
* *
2306 GTGACCGAGGCTCCCGCACCAAAGCTCGGTACTGTGCGGCA
129 GTGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
* *
2347 CTCCCGCCACCAATGGCCGGGGTTGCCGATGGTGACCGAGACA-CCGTCTGGGTTTGTCGATGGT
1 CTCCCG-CACCAATGGCCCGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
* *
2411 GACCGAGGCC-CCCGCCTTGGATTACCGATGGTGACCGAGGCGCACGCACACGGGGGCCTGATGG
65 GACCGAGGCCACCCGCCTAGGATTACCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGG
*
2475 TGAACG-GGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
130 TGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
**
2514 CTCCCGCACCAATGGCCCGGGGTTGCCGATGGTGACCGAGACACCC-TCTGTTTTTGCCGA-GGT
1 CTCCCGCACCAATGGCCC-GGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGT
2577 GACCGAGGC
65 GACCGAGGC
2586 ACGCACACGT
Statistics
Matches: 376, Mismatches: 23, Indels: 19
0.90 0.06 0.05
Matches are distributed among these distances:
166 48 0.13
167 154 0.41
168 52 0.14
169 79 0.21
170 43 0.11
ACGTcount: A:0.16, C:0.33, G:0.33, T:0.17
Consensus pattern (169 bp):
CTCCCGCACCAATGGCCCGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTG
ACCGAGGCCACCCGCCTAGGATTACCGATGGTGACCGAGGCTCACGCACACGGGGGCCTGATGGT
GACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCA
Found at i:17737 original size:33 final size:33
Alignment explanation
Indices: 17674--17758 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
17664 GGCCCGGGGG
* * *
17674 TTGCCGATGGTGACCGA-GACACCCGTCTGGGT
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
17706 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
1 TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
17739 TTGCCGATGGTGACCGAGGC
1 TTGCCGATGGTGACCGAGGC
17759 TCACGCACAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 17 0.35
33 32 0.65
ACGTcount: A:0.15, C:0.29, G:0.36, T:0.19
Consensus pattern (33 bp):
TTGCCGATGGTGACCGAGGCCACCCGCCTGGGA
Found at i:17916 original size:33 final size:32
Alignment explanation
Indices: 17843--17926 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 32
17833 TGGCCCGGGG
* * ** *
17843 TTGCCGATGGTGACCGA-GACCCCGTCTGGGT
1 TTGCCGATGGTGACCGAGGCCCCCGCCCAGGA
17874 TTGCCGATGGTGACCGAGGCCACCCGCCCAGGA
1 TTGCCGATGGTGACCGAGGCC-CCCGCCCAGGA
*
17907 TTGCCGATGGTGTCCGAGGC
1 TTGCCGATGGTGACCGAGGC
17927 TCACGCACAC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 17 0.38
32 2 0.04
33 26 0.58
ACGTcount: A:0.14, C:0.31, G:0.36, T:0.19
Consensus pattern (32 bp):
TTGCCGATGGTGACCGAGGCCCCCGCCCAGGA
Found at i:17929 original size:168 final size:169
Alignment explanation
Indices: 17606--18231 Score: 1042
Period size: 168 Copynumber: 3.7 Consensus size: 169
17596 GGGGGTTGCC
* *
17606 GATGGTGACCGAGGCTCCCGCACCAACGCCCGGTTCTGTGCGGCACTACCGCACCAATGGCCCGG
1 GATGGTGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCACTCCCGCACCAATGGCCC-G
*
17671 GGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGCCACCCGCCTG
65 GGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGCCACCCGCCTA
17736 GGATTGCCGATGGTGACCGAGGCTCACGCACAAGGGGCCT
130 GGATTGCCGATGGTGACCGAGGCTCACGCACAAGGGGCCT
*
17776 GATGGTGACCGAGACTCCCGCACCAACGCTCGGTTCTGTGCGGCACTCCCGCACCAATGGCCCGG
1 GATGGTGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCACTCCCGCACCAATGGCCCGG
*
17841 GGTTGCCGATGGTGACCGAGAC-CCCGTCTGGGTTTGCCGATGGTGACCGAGGCCACCCGCCCAG
66 GGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGCCACCCGCCTAG
* *
17905 GATTGCCGATGGTGTCCGAGGCTCACGCACACGGGGCCT
131 GATTGCCGATGGTGACCGAGGCTCACGCACAAGGGGCCT
* *
17944 GATGGTGACCGAGGCTCCCGCACCAAAGCTCGGTACTGTGCGGCACTCCCGCACCAATGG-CC-G
1 GATGGTGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCACTCCCGCACCAATGGCCCGG
* *
18007 GGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGTCGATGGTGACCGAGGCCACCCGCCTTG
66 GGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGCCACCCGCCTAG
* * *
18072 GATTACCGATGGTGACCGAGGCGCACGCACACGGGGGCCT
131 GATTGCCGATGGTGACCGAGGCTCACGCACA-AGGGGCCT
* *
18112 GATGGTGAACGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCACTCCCGCAACAATGGCCCGG
1 GATGGTGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCACTCCCGCACCAATGGCCCGG
**
18177 GGTTGCCGATGGTGACCGAGACACCCGTCTGTTTTTTGCCGATGGTGACCGAGGC
66 GGTTGCCGATGGTGACCGAGACACCCGTCTG-GGTTTGCCGATGGTGACCGAGGC
18232 ACGCACACGT
Statistics
Matches: 427, Mismatches: 24, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
166 23 0.05
167 69 0.16
168 197 0.46
169 26 0.06
170 92 0.22
171 20 0.05
ACGTcount: A:0.16, C:0.33, G:0.34, T:0.17
Consensus pattern (169 bp):
GATGGTGACCGAGGCTCCCGCACCAACGCTCGGTTCTGTGCGGCACTCCCGCACCAATGGCCCGG
GGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGCCACCCGCCTAG
GATTGCCGATGGTGACCGAGGCTCACGCACAAGGGGCCT
Found at i:18082 original size:33 final size:33
Alignment explanation
Indices: 18012--18093 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
18002 GGCCGGGTTG
* * * *
18012 CCGATGGTGACCGA-GACACCCGTCTGGGTTTG
1 CCGATGGTGACCGAGGCCACCCGCCTGGGATTA
* *
18044 TCGATGGTGACCGAGGCCACCCGCCTTGGATTA
1 CCGATGGTGACCGAGGCCACCCGCCTGGGATTA
18077 CCGATGGTGACCGAGGC
1 CCGATGGTGACCGAGGC
18094 GCACGCACAC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 13 0.31
33 29 0.69
ACGTcount: A:0.17, C:0.29, G:0.34, T:0.20
Consensus pattern (33 bp):
CCGATGGTGACCGAGGCCACCCGCCTGGGATTA
Found at i:26055 original size:11 final size:11
Alignment explanation
Indices: 26034--26064 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
26024 CGATAATGTC
26034 TCGCC-GAGCG
1 TCGCCGGAGCG
26044 TCGCCGGAGCG
1 TCGCCGGAGCG
26055 TCGCCGGAGC
1 TCGCCGGAGC
26065 ACCACCGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.10, C:0.39, G:0.42, T:0.10
Consensus pattern (11 bp):
TCGCCGGAGCG
Found at i:26480 original size:30 final size:32
Alignment explanation
Indices: 26446--26530 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 32
26436 CCAATGGCCC
26446 GGGTTTGCCGATGGTGACCGA-GACACCG-CT
1 GGGTTTGCCGATGGTGACCGAGGACACCGCCT
* *
26476 GGGTTTGCCGATGGTGACCGAGGCCCCCGCCT
1 GGGTTTGCCGATGGTGACCGAGGACACCGCCT
** *
26508 GGGACTGCCGATGGTGACTGAGG
1 GGGTTTGCCGATGGTGACCGAGG
26531 CTCACGCACA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 21 0.44
31 5 0.10
32 22 0.46
ACGTcount: A:0.14, C:0.27, G:0.40, T:0.19
Consensus pattern (32 bp):
GGGTTTGCCGATGGTGACCGAGGACACCGCCT
Done.