Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009473.1 Hibiscus syriacus cultivar Beakdansim tig00114184_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: 6433
ACGTcount: A:0.22, C:0.30, G:0.25, T:0.23
Found at i:6108 original size:92 final size:90
Alignment explanation
Indices: 5972--6137 Score: 262
Period size: 92 Copynumber: 1.8 Consensus size: 90
5962 CGCACCCGCG
* *
5972 CTCGGTTCTGTGCGCACTCCCGCACCATGGACTGGGGTTGCCGA-GCACCCTCGGTGTTGCCGAT
1 CTCGGCTCTGTGCGCACTCCCGCACCATGGACTGGGGTTGCCGAGGCACCCTCGGGGTTGCCGAT
6036 GGTGACCGAGGCCCCCGCACCCAACT
66 -GTGACCGAGGCCCCCGCACCCAACT
* *
6062 CTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCTCGGGGTTGCCG
1 CTCGGCTCTGTGC-GCACTCCCGCA-CCATGGACTGGGGTTGCCGAGGCACCCTCGGGGTTGCCG
6127 ATGTGACCGAG
64 ATGTGACCGAG
6138 ACACCCGTCT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
90 12 0.17
91 11 0.16
92 27 0.39
93 19 0.28
ACGTcount: A:0.11, C:0.37, G:0.33, T:0.19
Consensus pattern (90 bp):
CTCGGCTCTGTGCGCACTCCCGCACCATGGACTGGGGTTGCCGAGGCACCCTCGGGGTTGCCGAT
GTGACCGAGGCCCCCGCACCCAACT
Found at i:6124 original size:93 final size:94
Alignment explanation
Indices: 5972--6337 Score: 304
Period size: 93 Copynumber: 4.0 Consensus size: 94
5962 CGCACCCGCG
* * *
5972 CTCGGTTCTGTGC-GCACTCCCGCA-CCATGGACTGGGGTTGCCGA-GCACCC-TCGGTGTTGCC
1 CTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCC
6033 GATGGTGACCGAGGCCCCCGCACCCAACT
66 GATGGTGACCGAGGCCCCCGCACCCAACT
*
6062 CTCGGCTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCC-TCGGGGTTGCC
1 CTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCC
* *
6126 GAT-GTGACCGA-G-----ACACCC--GT
66 GATGGTGACCGAGGCCCCCGCACCCAACT
* * ** * * *
6146 CTGGGTTTGCCGATG-GTG-AC-CGAGACACCCTCTGGCTTGCCAATGG-TGCCGAGGCCACCCG
1 CTCGG-TT-CTG-TGCG-GCACTCCCG-CACCC-GTGGCCTG----GGGTTGCCGAGG-CACCCG
* * * * *
6207 CCTGGGATTGCCGATGGTGACCGA-GCCTCACGCAACCAACG
55 TC-GGGGTTGCCGATGGTGACCGAGGCC-CCCGCACCCAACT
6248 CTCGGTTCTGTGCGGCACTCCCGCACCCGT-GCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCC
1 CTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCC
6312 GATGGTGACCGAGGCCCCCCGCACCC
66 GATGGTGACCGAGG-CCCCCGCACCC
6338 GTGGCCTGGG
Statistics
Matches: 214, Mismatches: 31, Indels: 58
0.71 0.10 0.19
Matches are distributed among these distances:
84 5 0.02
85 3 0.01
86 15 0.07
87 9 0.04
90 20 0.09
91 19 0.09
92 27 0.13
93 50 0.23
94 26 0.12
95 10 0.05
98 4 0.02
99 4 0.02
100 14 0.07
101 4 0.02
102 4 0.02
ACGTcount: A:0.13, C:0.37, G:0.33, T:0.18
Consensus pattern (94 bp):
CTCGGTTCTGTGCGGCACTCCCGCACCCGTGGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCC
GATGGTGACCGAGGCCCCCGCACCCAACT
Found at i:6169 original size:32 final size:31
Alignment explanation
Indices: 6104--6231 Score: 138
Period size: 32 Copynumber: 4.2 Consensus size: 31
6094 CCTGGGGTTG
* *
6104 CCGAGGCACCCTC-GGGGTTGCCGAT-GTGA
1 CCGAGACACCCTCTGGGATTGCCGATGGTGA
*
6133 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCC-TCTGGGATTGCCGATGGTGA
* *
6165 CCGAGACACCCTCT-GGCTTGCCAATGGTG-
1 CCGAGACACCCTCTGGGATTGCCGATGGTGA
* *
6194 CCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGA-GACACCC-TCTGGGATTGCCGATGGTGA
6227 CCGAG
1 CCGAG
6232 CCTCACGCAA
Statistics
Matches: 84, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
29 14 0.17
30 21 0.25
31 16 0.19
32 29 0.35
33 4 0.05
ACGTcount: A:0.16, C:0.32, G:0.34, T:0.18
Consensus pattern (31 bp):
CCGAGACACCCTCTGGGATTGCCGATGGTGA
Found at i:6224 original size:62 final size:61
Alignment explanation
Indices: 6104--6231 Score: 168
Period size: 62 Copynumber: 2.1 Consensus size: 61
6094 CCTGGGGTTG
* * * * *
6104 CCGAGGCACCCTCGGGGTTGCCGATGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCTCGGGCTTGCCAATGTGACCGAGACACCCGCCTGGGATTGCCGATGGTGA
* *
6165 CCGAGACACCCTCTGGCTTGCCAATGGTG-CCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGAGACACCCTCGGGCTTGCCAAT-GTGACCGA-GACACCCGCCTGGGATTGCCGATGGTGA
6227 CCGAG
1 CCGAG
6232 CCTCACGCAA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
61 25 0.43
62 33 0.57
ACGTcount: A:0.16, C:0.32, G:0.34, T:0.18
Consensus pattern (61 bp):
CCGAGACACCCTCGGGCTTGCCAATGTGACCGAGACACCCGCCTGGGATTGCCGATGGTGA
Found at i:6324 original size:31 final size:31
Alignment explanation
Indices: 6289--6385 Score: 78
Period size: 30 Copynumber: 3.2 Consensus size: 31
6279 CCTGGGGTTG
6289 CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
1 CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
* *** *
6320 CCGAGGCCCCCCG-CACCCGTGGCC--TGGGTTG-
1 CCGAGG-CACCCGTC-GGGGTTGCCGAT-GG-TGA
6351 CCGAGGCACCCGTCGGGGTTGCCGAT-GTGA
1 CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
6381 CCGAG
1 CCGAG
6386 ACCCCGCACC
Statistics
Matches: 48, Mismatches: 10, Indels: 17
0.64 0.13 0.23
Matches are distributed among these distances:
29 2 0.04
30 17 0.35
31 16 0.33
32 13 0.27
ACGTcount: A:0.11, C:0.35, G:0.39, T:0.14
Consensus pattern (31 bp):
CCGAGGCACCCGTCGGGGTTGCCGATGGTGA
Found at i:6349 original size:62 final size:61
Alignment explanation
Indices: 6267--6390 Score: 214
Period size: 62 Copynumber: 2.0 Consensus size: 61
6257 GTGCGGCACT
*
6267 CCCGCACCCGTGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGGCCC
1 CCCGCACCCGTGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGAT-GTGACCGAGACCC
6329 CCCGCACCCGTGGCCT-GGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGTGACCGAGACCC
1 CCCGCACCCGT-GCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGTGACCGAGACCC
6390 C
1 C
6391 GCACCCCAAC
Statistics
Matches: 60, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
61 13 0.22
62 43 0.72
63 4 0.07
ACGTcount: A:0.10, C:0.38, G:0.37, T:0.15
Consensus pattern (61 bp):
CCCGCACCCGTGCCTGGGGTTGCCGAGGCACCCGTCGGGGTTGCCGATGTGACCGAGACCC
Done.