Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009527.1 Hibiscus syriacus cultivar Beakdansim tig00116012_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: 23416
ACGTcount: A:0.24, C:0.26, G:0.27, T:0.23
Found at i:54 original size:10 final size:10
Alignment explanation
Indices: 39--77 Score: 78
Period size: 10 Copynumber: 3.9 Consensus size: 10
29 TCCCGGTGGT
39 GCTCCGCGAC
1 GCTCCGCGAC
49 GCTCCGCGAC
1 GCTCCGCGAC
59 GCTCCGCGAC
1 GCTCCGCGAC
69 GCTCCGCGA
1 GCTCCGCGA
78 GACATTATCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.10, C:0.49, G:0.31, T:0.10
Consensus pattern (10 bp):
GCTCCGCGAC
Found at i:12813 original size:33 final size:32
Alignment explanation
Indices: 12749--12827 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 32
12739 GTGTGCGTGC
** * *
12749 GCCTCGGTCACCATCGGTAATCCAAGGCGGGT
1 GCCTCGGTCACCATCGACAAACCAAGACGGGT
*
12781 GGCCTCGGTCACCATCGACAAACCCAGACGGGT
1 -GCCTCGGTCACCATCGACAAACCAAGACGGGT
12814 --CTCGGTCACCATCG
1 GCCTCGGTCACCATCG
12828 GCAACCCCGG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 14 0.34
33 27 0.66
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.16
Consensus pattern (32 bp):
GCCTCGGTCACCATCGACAAACCAAGACGGGT
Found at i:12979 original size:33 final size:32
Alignment explanation
Indices: 12915--12998 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 32
12905 GTGTGCGTGA
* * ** *
12915 GCCTCGGACACCATCGGCAATCCTGGGCGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGT
12947 GGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 -GCCTCGGTCACCATCGGCAAACCCAGACGGGT
*
12980 GTCTCGGTCA-CATCGGCAA
1 GCCTCGGTCACCATCGGCAA
12999 CCCGGGCCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 9 0.20
32 9 0.20
33 27 0.60
ACGTcount: A:0.19, C:0.35, G:0.31, T:0.15
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGT
Found at i:13001 original size:167 final size:170
Alignment explanation
Indices: 12613--13188 Score: 979
Period size: 167 Copynumber: 3.4 Consensus size: 170
12603 ACGTGTGCGT
**
12613 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
12678 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTC-GTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* *
12742 TGCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
12782 GCCTCGGTCACCATCGACAAACCCAGAC-GG-GTCTCGGTCACCATCGGCAACCCC-GGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
12844 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCA-CAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* **
12908 TGCGTGAGCCTCGGACACCATCGGCAATCCTGGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
12948 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCA-CATCGGCAA-CCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
13011 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG-CCCCTTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
*
13075 TGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
13115 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
13180 GTGCGGGAG
66 GTGCGGGAG
13189 CCTCGGTCAC
Statistics
Matches: 382, Mismatches: 18, Indels: 14
0.92 0.04 0.03
Matches are distributed among these distances:
166 127 0.33
167 184 0.48
168 25 0.07
169 46 0.12
ACGTcount: A:0.17, C:0.34, G:0.33, T:0.16
Consensus pattern (170 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:13124 original size:33 final size:32
Alignment explanation
Indices: 13082--13306 Score: 188
Period size: 32 Copynumber: 6.7 Consensus size: 32
13072 TTGTGCGTGA
13082 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAA-CCCAGGCGGGTG
*
13115 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGC-AACCCAGGCGGGTG
* * *
13147 GTCTCGGTCACCATCGGCAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAA-CCCAGG-C----G-G-GTG
** * *
13187 AGCCTCGGTCACCATCAGGC--CCCTTGTGCGTG
1 -GCCTCGGTCACCATC-GGCAACCCAGGCGGGTG
*
13219 AGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCA-ACCCAGGCGGGTG
* *
13253 GCCTCGGTCACCATCGGCAAACCAGACGGGT-
1 GCCTCGGTCACCATCGGCAACCCAGGCGGGTG
*
13284 GTCTCGGTCACCATCGGCAACCC
1 GCCTCGGTCACCATCGGCAACCC
13307 CGGGCCATTG
Statistics
Matches: 157, Mismatches: 20, Indels: 32
0.75 0.10 0.15
Matches are distributed among these distances:
31 26 0.17
32 48 0.31
33 48 0.31
34 11 0.07
37 1 0.01
38 1 0.01
39 5 0.03
41 14 0.09
42 3 0.02
ACGTcount: A:0.16, C:0.37, G:0.31, T:0.16
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAACCCAGGCGGGTG
Found at i:13127 original size:65 final size:65
Alignment explanation
Indices: 13052--13267 Score: 231
Period size: 65 Copynumber: 3.2 Consensus size: 65
13042 GTGCGGGAGT
13052 CTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
* * * * * * *
13117 CTCGGTCACCATC-GGCAAACCC-AG-ACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATT
1 CTCGGTCACCATCAGGC---CCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGG-C---
*
13179 GGTGCGGGAGC
59 -G-G-GTG-GC
*
13190 CTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTGGC
1 CTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
13255 CTCGGTCACCATC
1 CTCGGTCACCATC
13268 GGCAAACCAG
Statistics
Matches: 120, Mismatches: 17, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
64 3 0.03
65 55 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 41 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:13208 original size:138 final size:137
Alignment explanation
Indices: 13039--13322 Score: 541
Period size: 138 Copynumber: 2.1 Consensus size: 137
13029 GAACCGAGCG
*
13039 TTGGTGCGGGAGTCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
1 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
13104 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
66 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAA-CCAGACGGGTGTCTCGGTCACCATCGGCAACC
13169 CCGGGCCA
130 CCGGGCCA
*
13177 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAGTC
1 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
13242 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCAGACGGGTGTCTCGGTCACCATCGGCAACCC
66 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCAGACGGGTGTCTCGGTCACCATCGGCAACCC
13307 CGGGCCA
131 CGGGCCA
13314 TTGGTGCGG
1 TTGGTGCGG
13323 TAGTGCCGCA
Statistics
Matches: 144, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
137 49 0.34
138 95 0.66
ACGTcount: A:0.15, C:0.35, G:0.32, T:0.18
Consensus pattern (137 bp):
TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAATC
CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCAGACGGGTGTCTCGGTCACCATCGGCAACCC
CGGGCCA
Found at i:13293 original size:31 final size:32
Alignment explanation
Indices: 13220--13303 Score: 116
Period size: 31 Copynumber: 2.6 Consensus size: 32
13210 TTGTGCGTGA
** *
13220 GCCTCGGTCACCATCGGCAGTCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCA-AACCAGACGGGTG
13253 GCCTCGGTCACCATCGGCAAACCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAGACGGGTG
*
13284 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
13304 CCCCGGGCCA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
31 19 0.40
32 9 0.19
33 19 0.40
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.15
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAAACCAGACGGGTG
Found at i:13707 original size:11 final size:11
Alignment explanation
Indices: 13693--13724 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
13683 TCCCGGTGGT
13693 GCTCCGGCGAC
1 GCTCCGGCGAC
13704 GCTCCGGCGAC
1 GCTCCGGCGAC
13715 GCTCCGGCGA
1 GCTCCGGCGA
13725 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.