Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008963.1 Hibiscus syriacus cultivar Beakdansim tig00112304_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: 30200
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Found at i:6752 original size:33 final size:32
Alignment explanation
Indices: 6715--6799 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 32
6705 GTGTGCGTGC
* * *
6715 GCCTCGGTCACCATCGGTAATCCAAGGCGGGT
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGT
* *
6747 GGCCTCGGTCACCATCGACAAACCCAGACGGGT
1 -GCCTCGGTCACCATCGGCAAACCAAGACGGGT
*
6780 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
6800 CCCGGCCATT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 18 0.40
33 27 0.60
ACGTcount: A:0.21, C:0.34, G:0.28, T:0.16
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAAACCAAGACGGGT
Found at i:6837 original size:168 final size:170
Alignment explanation
Indices: 6578--7158 Score: 999
Period size: 168 Copynumber: 3.4 Consensus size: 170
6568 ACGTGTGCGT
**
6578 GCCTCGGTCACCATCGGCAAAAAACAGACGGGTGTCTCGGTCACCATCGGCAA-CCCGGGCCATT
1 GCCTCGGTCACCATCGGC-AAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATT
*
6642 GGTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGTTCACCATCAGGCCCCCGT
65 GGTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGT
* *
6707 GTGCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
130 GTGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
6748 GCCTCGGTCACCATCGACAAACCCAGACGGGTGTCTCGGTCACCATCGGCAA-CCC-GGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
6811 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
**
6876 TGCGTGAGCCTCGGTCACCATCGGCAATCCTGGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
6916 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
6981 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG-CCCCTTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
*
7045 TGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
7085 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
7150 GTGCGGGAG
66 GTGCGGGAG
7159 CCTCGGTCAC
Statistics
Matches: 391, Mismatches: 18, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
168 157 0.40
169 155 0.40
170 79 0.20
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (170 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:6959 original size:32 final size:33
Alignment explanation
Indices: 6883--6967 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
6873 GTGTGCGTGA
* ** *
6883 GCCTCGGTCACCATCGGCAATCCTGGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
6916 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
*
6948 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
6968 CCCCGGGCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 19 0.40
33 28 0.60
ACGTcount: A:0.18, C:0.35, G:0.31, T:0.16
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
Found at i:7094 original size:33 final size:33
Alignment explanation
Indices: 7052--7274 Score: 186
Period size: 33 Copynumber: 6.6 Consensus size: 33
7042 TTGTGCGTGA
*
7052 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
7085 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
* * * * *
7117 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG
** * *
7157 AGCCTCGGTCACCATCAGGC---CCCTTGTGCGTG
1 -GCCTCGGTCACCATC-GGCAAACCCAGGCGGGTG
**
7189 AGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
7223 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
7255 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
7275 CCCCGGGCCA
Statistics
Matches: 154, Mismatches: 23, Indels: 27
0.75 0.11 0.13
Matches are distributed among these distances:
31 3 0.02
32 59 0.38
33 60 0.39
34 9 0.06
37 1 0.01
38 1 0.01
39 5 0.03
41 14 0.09
42 2 0.01
ACGTcount: A:0.17, C:0.36, G:0.31, T:0.17
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
Found at i:7098 original size:65 final size:65
Alignment explanation
Indices: 7022--7237 Score: 222
Period size: 65 Copynumber: 3.2 Consensus size: 65
7012 GTGCGGGAGT
7022 CTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
* * * * * * * *
7087 CTCGGTCACCATC-GGCAAACCC-AG-ACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATT
1 CTCGGTCACCATCAGGC---CCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGG-C---
*
7149 GGTGCGGGAGC
59 -G-G-GTG-GC
*
7160 CTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTGGC
1 CTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
7225 CTCGGTCACCATC
1 CTCGGTCACCATC
7238 GGCAAACCCA
Statistics
Matches: 118, Mismatches: 19, Indels: 28
0.72 0.12 0.17
Matches are distributed among these distances:
64 3 0.03
65 54 0.46
66 4 0.03
67 4 0.03
68 1 0.01
70 1 0.01
71 4 0.03
72 4 0.03
73 40 0.34
74 3 0.03
ACGTcount: A:0.15, C:0.37, G:0.31, T:0.18
Consensus pattern (65 bp):
CTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
Found at i:7128 original size:32 final size:32
Alignment explanation
Indices: 7052--7274 Score: 182
Period size: 32 Copynumber: 6.6 Consensus size: 32
7042 TTGTGCGTGA
*
7052 GCCTCGGTCACCATCGGCAATCCCAGGCGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGT
*
7084 GGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGT
* * * *
7117 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGGA
1 GCCTCGGTCACCATCGGCAA--AC---CCA---G-GCGGGT
* * *
7158 GCCTCGGTCACCATCAGGC---CCCTTGTGCGTGA
1 GCCTCGGTCACCATC-GGCAAACCC-AG-GCGGGT
**
7190 GCCTCGGTCACCATCGGCAGTCCCAGGCGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGT
*
7222 GGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGT
*
7255 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
7275 CCCCGGGCCA
Statistics
Matches: 157, Mismatches: 18, Indels: 31
0.76 0.09 0.15
Matches are distributed among these distances:
31 3 0.02
32 63 0.40
33 60 0.38
34 6 0.04
37 4 0.03
40 1 0.01
41 18 0.11
42 2 0.01
ACGTcount: A:0.17, C:0.36, G:0.31, T:0.17
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAAACCCAGGCGGGT
Found at i:7173 original size:138 final size:138
Alignment explanation
Indices: 7009--7296 Score: 549
Period size: 138 Copynumber: 2.1 Consensus size: 138
6999 GAACCGAGCG
*
7009 TTGGTGCGGGAGTCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
1 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
*
7074 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGTAACC
66 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
7139 CCGGGCCA
131 CCGGGCCA
*
7147 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAGTC
1 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
7212 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
66 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
7277 CCGGGCCA
131 CCGGGCCA
7285 TTGGTGCGGGAG
1 TTGGTGCGGGAG
7297 TGCCGCACAG
Statistics
Matches: 147, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
138 147 1.00
ACGTcount: A:0.15, C:0.34, G:0.33, T:0.18
Consensus pattern (138 bp):
TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
CCGGGCCA
Found at i:12683 original size:11 final size:11
Alignment explanation
Indices: 12669--12700 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
12659 TCCCGGTGGT
12669 GCTCCGGCGAC
1 GCTCCGGCGAC
12680 GCTCCGGCGAC
1 GCTCCGGCGAC
12691 GCTCCGGCGA
1 GCTCCGGCGA
12701 GACATTATCG
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:0.44, G:0.38, T:0.09
Consensus pattern (11 bp):
GCTCCGGCGAC
Found at i:18950 original size:11 final size:11
Alignment explanation
Indices: 18936--18967 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
18926 TCCCGGTGGT
18936 GCTCCGGCGAC
1 GCTCCGGCGAC
18947 GCTCCGGCGAC
1 GCTCCGGCGAC
18958 GCTCCGGCGA
1 GCTCCGGCGA
18968 GACATTATCG
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:0.44, G:0.38, T:0.09
Consensus pattern (11 bp):
GCTCCGGCGAC
Found at i:27046 original size:33 final size:32
Alignment explanation
Indices: 27009--27093 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 32
26999 GTGTGCGTGC
* *
27009 GCCTCGGTCACCATCGGTAATCCAAGGCGGGT
1 GCCTCGGTCACCATCGGTAAACCAAGACGGGT
** *
27041 GGCCTCGGTCACCATCGACAAACCCAGACGGGT
1 -GCCTCGGTCACCATCGGTAAACCAAGACGGGT
*
27074 GTCTCGGTCACCATCGGTAA
1 GCCTCGGTCACCATCGGTAA
27094 CCCCGGCCAC
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 17 0.39
33 27 0.61
ACGTcount: A:0.21, C:0.33, G:0.28, T:0.18
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGTAAACCAAGACGGGT
Found at i:27303 original size:33 final size:33
Alignment explanation
Indices: 27261--27480 Score: 177
Period size: 33 Copynumber: 6.6 Consensus size: 33
27251 TTGTGCGTGA
*
27261 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
27294 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
* * *
27326 GTCTC-GTCACCATCGGCAACCCGGGCCATTGGTGCGGG-A
1 GCCTCGGTCACCATCGGCAA-AC---CCA---G-GCGGGTG
** * *
27365 GCCTCGGTCACCATCAGGC---CCCTTGTGCGTG
1 GCCTCGGTCACCATC-GGCAAACCCAGGCGGGTG
**
27396 AG-CTCGGTCACCATCGGCAGTCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
27429 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
27461 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
27481 CCGGGCATTG
Statistics
Matches: 151, Mismatches: 19, Indels: 35
0.74 0.09 0.17
Matches are distributed among these distances:
30 6 0.04
31 27 0.18
32 26 0.17
33 65 0.43
34 2 0.01
35 3 0.02
37 1 0.01
38 1 0.01
39 8 0.05
40 9 0.06
41 3 0.02
ACGTcount: A:0.17, C:0.36, G:0.31, T:0.16
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
Found at i:27375 original size:104 final size:104
Alignment explanation
Indices: 27253--27448 Score: 247
Period size: 104 Copynumber: 1.9 Consensus size: 104
27243 CAGGCCCCTT
* *
27253 GTGCGTGAGCCTCGGTCACCATC-GGCAATCCCAGGCGGGTG-GCCTCGGTCACCATCGGCAAAC
1 GTGCGGGAGCCTCGGTCACCATCAGGC---CCCAGGCGCGTGAG-CTCGGTCACCATCGGCAAAC
*
27316 CCAGACGGGT-GTCTC-GTCACCATCGGCAACCCGGGCCATTG
62 CCAGACGGGTGGCCTCGGTCACCATCGGCAACCCGGGCCATTG
** * **
27357 GTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCTCGGTCACCATCGGCAGTCCCAG
1 GTGCGGGAGCCTCGGTCACCATCAGGCCCCAGGCGCGTGAGCTCGGTCACCATCGGCAAACCCAG
*
27422 GCGGGTGGCCTCGGTCACCATCGGCAA
66 ACGGGTGGCCTCGGTCACCATCGGCAA
27449 ACCCAGACGG
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
102 35 0.44
103 5 0.06
104 36 0.46
105 3 0.04
ACGTcount: A:0.16, C:0.35, G:0.32, T:0.17
Consensus pattern (104 bp):
GTGCGGGAGCCTCGGTCACCATCAGGCCCCAGGCGCGTGAGCTCGGTCACCATCGGCAAACCCAG
ACGGGTGGCCTCGGTCACCATCGGCAACCCGGGCCATTG
Found at i:27441 original size:135 final size:135
Alignment explanation
Indices: 27209--27496 Score: 499
Period size: 135 Copynumber: 2.1 Consensus size: 135
27199 TGCCGCACAG
* * *
27209 AACCGAGCGTTGGTGCGGGAGTATCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCA
1 AACCGGGCATTGGTGCGGGAGCATCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCA
27274 TCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTC-GTCACCA
66 TCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCA
27338 TCGGC
131 TCGGC
*
27343 AACCCGGGCCATTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAG-CTCGGTCAC
1 AA-CCGGG-CATTGGTGCGGGAGCATCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCAC
*
27407 CATCGGCAGTCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCAC
64 CATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCAC
27472 CATCGGC
129 CATCGGC
27479 AACCGGGCATTGGTGCGG
1 AACCGGGCATTGGTGCGG
27497 AGTGCCGCAC
Statistics
Matches: 146, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
134 13 0.09
135 76 0.52
136 57 0.39
ACGTcount: A:0.16, C:0.34, G:0.33, T:0.17
Consensus pattern (135 bp):
AACCGGGCATTGGTGCGGGAGCATCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCA
TCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCA
TCGGC
Found at i:27879 original size:11 final size:11
Alignment explanation
Indices: 27865--27896 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
27855 TCCCGGTGGT
27865 GCTCCGGCGAC
1 GCTCCGGCGAC
27876 GCTCCGGCGAC
1 GCTCCGGCGAC
27887 GCTCCGGCGA
1 GCTCCGGCGA
27897 GACATTATCG
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:0.44, G:0.38, T:0.09
Consensus pattern (11 bp):
GCTCCGGCGAC
Done.