Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009526.1 Hibiscus syriacus cultivar Beakdansim tig00115995_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: 12034
ACGTcount: A:0.23, C:0.26, G:0.30, T:0.22
Found at i:6762 original size:33 final size:31
Alignment explanation
Indices: 6725--6812 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 31
6715 GCGTGAGCCC
6725 CGGTCACCATCGGCAATCCCAGGCGGGTGGCCT
1 CGGTCACCATCGGCAA-CCCAGGCGGGT-GCCT
* ** *
6758 CGGTCACCATCGGCAAAACCATACGGGTGTCT
1 CGGTCACCATCGGC-AACCCAGGCGGGTGCCT
6790 CGGTCACCATCGGCAACCCAGGC
1 CGGTCACCATCGGCAACCCAGGC
6813 CATTGGTGAG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 6 0.13
32 17 0.36
33 22 0.47
34 2 0.04
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.15
Consensus pattern (31 bp):
CGGTCACCATCGGCAACCCAGGCGGGTGCCT
Found at i:6974 original size:63 final size:63
Alignment explanation
Indices: 6857--6989 Score: 198
Period size: 63 Copynumber: 2.1 Consensus size: 63
6847 TGGTGCGTGA
*
6857 GGCTCGGTCACCATCGGCAACCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GGCTCGGTCACCATCGGCAACCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
* * *
6920 GTCTCGGTCACCATCGGCAAACCCAGACGGGT-GTCTCGGTCACCATCGGC-AACCCCGACGGGT
1 GGCTCGGTCACCATCGGC-AA-CCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
6983 GGCTCGG
1 GGCTCGG
6990 CAACCCCAGG
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
63 35 0.56
64 19 0.30
65 9 0.14
ACGTcount: A:0.18, C:0.35, G:0.32, T:0.14
Consensus pattern (63 bp):
GGCTCGGTCACCATCGGCAACCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
Found at i:6980 original size:31 final size:32
Alignment explanation
Indices: 6859--6989 Score: 196
Period size: 32 Copynumber: 4.2 Consensus size: 32
6849 GTGCGTGAGG
* *
6859 CTCGGTCACCATCGGC-AA-CCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
6890 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
6922 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* *
6954 CTCGGTCACCATCGGC-AACCCCGACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
6985 CTCGG
1 CTCGG
6990 CAACCCCAGG
Statistics
Matches: 94, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
31 34 0.36
32 51 0.54
33 9 0.10
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.15
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:7112 original size:31 final size:31
Alignment explanation
Indices: 7072--7169 Score: 92
Period size: 31 Copynumber: 3.1 Consensus size: 31
7062 GCAACCCCGA
7072 CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
1 CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
* * * ****
7103 CGGGGGCCTCGGTC-ACCATC-GGCAACCCCCG
1 CGGGTGCCTCGG-CAACC-CCAGGCCACGGGTG
7134 ACGGGTGCCTCGGCAACCCCAGGCCACGGGTG
1 -CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
7166 CGGG
1 CGGG
7170 AGTGCCGCAC
Statistics
Matches: 48, Mismatches: 14, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
31 26 0.54
32 22 0.46
ACGTcount: A:0.13, C:0.40, G:0.38, T:0.09
Consensus pattern (31 bp):
CGGGTGCCTCGGCAACCCCAGGCCACGGGTG
Found at i:7113 original size:62 final size:63
Alignment explanation
Indices: 7036--7169 Score: 252
Period size: 63 Copynumber: 2.1 Consensus size: 63
7026 AGCGAGAGTT
*
7036 GGGTGCGGGGTCCTCGGTCACCATCGGCAA-CCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
7098 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
7161 GGGTGCGGG
1 GGGTGCGGG
7170 AGTGCCGCAC
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
62 29 0.41
63 41 0.59
ACGTcount: A:0.13, C:0.39, G:0.37, T:0.10
Consensus pattern (63 bp):
GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
Found at i:7145 original size:94 final size:94
Alignment explanation
Indices: 6922--7146 Score: 244
Period size: 94 Copynumber: 2.4 Consensus size: 94
6912 AGACGGGTGT
* *
6922 CTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGACGGGTGGCT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCCGACGGGTGCCT
6987 CGGCAACCCCAGGCCACGGGTGCGGGGAG
66 CGGCAACCCCAGGCCACGGGTGCGGGGAG
* * * * ***** *
7016 TTCCGGACA-GAGC-G-AGAGTTGGGTGCGGG-GTCCTCGGTCACCATCGGCAACCCCGACGGGT
1 CT-CGGTCACCATCGGCA-AACCCAG-ACGGGTG-CCTCGGTCACCATCGGCAACCCCGACGGGT
7077 GCCTCGGCAACCCCAGGCCACGGGTGCGGGG-G
62 GCCTCGGCAACCCCAGGCCACGGGTGCGGGGAG
* *
7109 CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
1 -CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGG
7147 CAACCCCAGG
Statistics
Matches: 100, Mismatches: 22, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
92 1 0.01
93 10 0.10
94 79 0.79
95 9 0.09
96 1 0.01
ACGTcount: A:0.16, C:0.36, G:0.36, T:0.12
Consensus pattern (94 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAACCCCGACGGGTGCCT
CGGCAACCCCAGGCCACGGGTGCGGGGAG
Found at i:7244 original size:32 final size:32
Alignment explanation
Indices: 7203--7334 Score: 178
Period size: 32 Copynumber: 4.2 Consensus size: 32
7193 GTGCGTGAGG
* * *
7203 CTCGGTCACCATCGGCAATCCCAG-GGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
*
7235 CTCGGTCACCAT-GGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
7266 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* * *
7298 CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
7330 CTCGG
1 CTCGG
7335 CAACCCCAGG
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
31 22 0.24
32 68 0.76
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.15
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:7270 original size:156 final size:155
Alignment explanation
Indices: 6887--7302 Score: 513
Period size: 156 Copynumber: 2.7 Consensus size: 155
6877 CCAGGCGGGT
* *
6887 GGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GGCCTCGGTCACCATCGGC-AACCCAGACGGGTGCCTCGGTCACCAT-GGCAAAGCCAGACGGGT
*
6952 GTCTCGGTCACCATCGGCAACCCCGACGGGTGGCTCGGCAACCCCAGGCCACGGGTGCGGGGAGT
64 GTCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGAGT
* * *
7017 TCCGGACAGAGCGAGAGTTGGGTGCGG
129 GCCGCACAGAACGAGAGTTGGGTGCGG
* * * ***
7044 GGTCCTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGG-CAACCCCA-GGCCACGGGTG-CGG
1 GG-CCTCGGTCACCATCGGCAACCCAGACGGGTGCCTCGGTC-A--CCATGGCAAAGCCAGACGG
* *
7106 GGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGC-GGG
62 GTGTCTCGGTCACCATCGGCAA-CCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGG
*
7170 AGTGCCGCACAGAACGAGCGTT-GGTGCGTG
126 AGTGCCGCACAGAACGAGAGTTGGGTGCG-G
*
7200 AGG-CTCGGTCACCATCGGCAATCCCAG-GGGGTGGCCTCGGTCACCATGGCAAAGCCAGACGGG
1 -GGCCTCGGTCACCATCGGCAA-CCCAGACGGGT-GCCTCGGTCACCATGGCAAAGCCAGACGGG
* *
7263 TGTCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGG
63 TGTCTCGGTCACCATCGGC-AACCCCGACGGGTGCCTCGG
7303 TCACCATCGG
Statistics
Matches: 220, Mismatches: 26, Indels: 27
0.81 0.10 0.10
Matches are distributed among these distances:
154 3 0.01
155 34 0.15
156 95 0.43
157 68 0.31
158 17 0.08
159 3 0.01
ACGTcount: A:0.18, C:0.34, G:0.35, T:0.13
Consensus pattern (155 bp):
GGCCTCGGTCACCATCGGCAACCCAGACGGGTGCCTCGGTCACCATGGCAAAGCCAGACGGGTGT
CTCGGTCACCATCGGCAACCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGGAGTGC
CGCACAGAACGAGAGTTGGGTGCGG
Found at i:7281 original size:63 final size:64
Alignment explanation
Indices: 7203--7334 Score: 178
Period size: 63 Copynumber: 2.1 Consensus size: 64
7193 GTGCGTGAGG
* * * *
7203 CTCGGTCACCATCGGCAATCCCAG-GGGGTGGCCTCGGTCACCAT-GGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GCCTCGGTCACCATCGGCAAACCCAGACGGGTGC
* * *
7266 CTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAAACCCAGACGGGTGC
7330 CTCGG
1 CTCGG
7335 CAACCCCAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
63 36 0.60
64 24 0.40
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.15
Consensus pattern (64 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATCGGCAAACCCAGACGGGTGC
Done.