Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009483.1 Hibiscus syriacus cultivar Beakdansim tig00114533_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: 23562
ACGTcount: A:0.23, C:0.26, G:0.29, T:0.22
Found at i:6797 original size:32 final size:31
Alignment explanation
Indices: 6758--6844 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
6748 GCGTGAGCCC
*
6758 CGGTCACCATC-GCAATCCCAGGCGGGTGGCCT
1 CGGTCACCATCGGCAAACCCAGGC-GGT-GCCT
* ** *
6790 CGGTCACCATCGGCAAAACCATACGGTGTCT
1 CGGTCACCATCGGCAAACCCAGGCGGTGCCT
*
6821 CGGTCACCATCGGCAACCCCAGGC
1 CGGTCACCATCGGCAAACCCAGGC
6845 CATTGGTGAG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
31 23 0.51
32 14 0.31
33 8 0.18
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (31 bp):
CGGTCACCATCGGCAAACCCAGGCGGTGCCT
Found at i:6929 original size:31 final size:32
Alignment explanation
Indices: 6891--7018 Score: 160
Period size: 31 Copynumber: 4.2 Consensus size: 32
6881 GTGCGTGAGG
* *
6891 CTCGGTCACCATC-GC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
6922 CTCGGTCACCATCGGCAAACCCAGAC-GGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
6953 CTC-GTCACCATC-GCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* * *
6983 CTCGGTCACCATCGGCAACCCCCGAC-GGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
7014 CTCGG
1 CTCGG
7019 CAACCCCAGG
Statistics
Matches: 87, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
29 12 0.14
30 17 0.20
31 35 0.40
32 15 0.17
33 8 0.09
ACGTcount: A:0.19, C:0.38, G:0.28, T:0.15
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:6990 original size:61 final size:61
Alignment explanation
Indices: 6889--7017 Score: 188
Period size: 61 Copynumber: 2.1 Consensus size: 61
6879 TGGTGCGTGA
*
6889 GGCTCGGTCACCATCGCAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGT
1 GGCTC-GTCACCATCGCAACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGT
* * * *
6951 GTCTCGTCACCATCGCAAACCCAGACGGGT-GTCTCGGTCACCATCGGCAACCCCCGACGGT
1 GGCTCGTCACCATCGC-AACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGT
7012 GGCTCG
1 GGCTCG
7018 GCAACCCCAG
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
61 44 0.73
62 16 0.27
ACGTcount: A:0.19, C:0.38, G:0.29, T:0.15
Consensus pattern (61 bp):
GGCTCGTCACCATCGCAACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGT
Found at i:7159 original size:60 final size:61
Alignment explanation
Indices: 7064--7194 Score: 230
Period size: 60 Copynumber: 2.1 Consensus size: 61
7054 GCCGAGAGTT
7064 GGGTGCGGGGTCCTCGGTCACCATCGGCAACCCCCGAC-GGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGC-GGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTC-GCAACCCCAGGCCAC
7126 GGGTGCGGG-CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACCCCAGGCCAC
1 GGGTGCGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACCCCAGGCCAC
7186 GGGTGCGGG
1 GGGTGCGGG
7195 AGTGCCGCAC
Statistics
Matches: 68, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
60 51 0.75
61 11 0.16
62 6 0.09
ACGTcount: A:0.14, C:0.40, G:0.35, T:0.11
Consensus pattern (61 bp):
GGGTGCGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGCAACCCCAGGCCAC
Found at i:7303 original size:32 final size:32
Alignment explanation
Indices: 7229--7361 Score: 185
Period size: 32 Copynumber: 4.1 Consensus size: 32
7219 GTGCGTGAGG
* *
7229 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
7262 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
*
7294 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
* *
7326 CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
7358 CTCG
1 CTCG
7362 CAACCCCAGG
Statistics
Matches: 90, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
32 64 0.71
33 26 0.29
ACGTcount: A:0.18, C:0.36, G:0.30, T:0.16
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:15664 original size:33 final size:32
Alignment explanation
Indices: 15627--15715 Score: 115
Period size: 33 Copynumber: 2.8 Consensus size: 32
15617 GCGTGAGCCC
*
15627 CGGTCACCATCGGCAATCCCAGGCGGGTGGCCT
1 CGGTCACCATCGGCAAACCCAGGCGGGT-GCCT
* ** *
15660 CGGTCACCATCGGCAAAACCATACGGGTGTCT
1 CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
*
15692 CGGTCACCATCGGCAACCCCAGGC
1 CGGTCACCATCGGCAAACCCAGGC
15716 CATTGGTGAG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 23 0.49
33 24 0.51
ACGTcount: A:0.20, C:0.37, G:0.28, T:0.15
Consensus pattern (32 bp):
CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
Found at i:15859 original size:31 final size:32
Alignment explanation
Indices: 15762--15892 Score: 187
Period size: 32 Copynumber: 4.2 Consensus size: 32
15752 GTGCGTGAGG
* *
15762 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
15794 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
15826 CTCGGTCACCATCGGCAAACCCAGAC-GGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* * *
15857 CTCGGTCACCATC-GCAACCCCCGACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
15888 CTCGG
1 CTCGG
15893 CAACCCCAGG
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
30 10 0.11
31 27 0.29
32 43 0.47
33 12 0.13
ACGTcount: A:0.18, C:0.37, G:0.30, T:0.15
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:15985 original size:32 final size:32
Alignment explanation
Indices: 15944--16049 Score: 103
Period size: 32 Copynumber: 3.4 Consensus size: 32
15934 GAGTTGGGTG
15944 CGGGT-CCTCGGTCACCATCGGCAACCCCCGA
1 CGGGTGCCTCGGTCACCATCGGCAACCCCCGA
* * ****
15975 CGGGTGCCTCGG-CAACC-CCAGGCCACGGGTG-
1 CGGGTGCCTCGGTC-ACCATC-GGCAACCCCCGA
*
16006 CGGGGGCCTCGGTCACCATCGGCAACCCCCGA
1 CGGGTGCCTCGGTCACCATCGGCAACCCCCGA
16038 CGGGTGCCTCGG
1 CGGGTGCCTCGG
16050 CAACCCCAGG
Statistics
Matches: 55, Mismatches: 14, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
31 27 0.49
32 28 0.51
ACGTcount: A:0.13, C:0.42, G:0.34, T:0.11
Consensus pattern (32 bp):
CGGGTGCCTCGGTCACCATCGGCAACCCCCGA
Found at i:16037 original size:63 final size:63
Alignment explanation
Indices: 15939--16071 Score: 243
Period size: 63 Copynumber: 2.1 Consensus size: 63
15929 GCCGAGAGTT
*
15939 GGGTGC-GGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
16001 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
16064 -GGTGCGGG
1 GGGTGCGGG
16072 AGTGCCGCAC
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
62 14 0.20
63 55 0.80
ACGTcount: A:0.14, C:0.40, G:0.36, T:0.11
Consensus pattern (63 bp):
GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
Found at i:16042 original size:94 final size:92
Alignment explanation
Indices: 15826--16049 Score: 229
Period size: 94 Copynumber: 2.4 Consensus size: 92
15816 AGACGGGTGT
*
15826 CTCGGTCACCATCGGCAAACCCAGACGGTGT-CTCGGTCACCATCGCAACCCCCGACGGGTGGCT
1 CTCGGTCACCATCGGCAAACCCAGACGG-GTCCTCGGTCACCATCGCAACCCCCGACGGGTGCCT
15890 CGGCAACCCCAGGCCACGGGTGCGGGAG
65 CGGCAACCCCAGGCCACGGGTGCGGGAG
* * * * * ***** *
15918 TTCCGGACA-GAGCCG-AGAGTTGGGTGCGGGTCCTCGGTCACCATCGGCAACCCCCGACGGGTG
1 CT-CGGTCACCATCGGCA-AACCCAG-ACGGGTCCTCGGTCACCATC-GCAACCCCCGACGGGTG
*
15981 CCTCGGCAACCCCAGGCCACGGGTGCGGGGG
62 CCTCGGCAACCCCAGGCCACGGGTGCGGGAG
* *
16012 CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG
1 -CTCGGTCACCATCGGCAAACCCAGACGGGT-CCTCGG
16050 CAACCCCAGG
Statistics
Matches: 99, Mismatches: 24, Indels: 15
0.72 0.17 0.11
Matches are distributed among these distances:
91 1 0.01
92 8 0.08
93 21 0.21
94 56 0.57
95 12 0.12
96 1 0.01
ACGTcount: A:0.16, C:0.38, G:0.34, T:0.12
Consensus pattern (92 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTCCTCGGTCACCATCGCAACCCCCGACGGGTGCCTC
GGCAACCCCAGGCCACGGGTGCGGGAG
Found at i:16180 original size:32 final size:32
Alignment explanation
Indices: 16106--16237 Score: 178
Period size: 32 Copynumber: 4.2 Consensus size: 32
16096 GTGCGTGAGG
* *
16106 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GC
* * *
16139 CTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
16171 CTCGGTCACCATCGGCAAACCCAGACGGGT--
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
* *
16201 CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGC
16233 CTCGG
1 CTCGG
16238 CAACCCCAGG
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
30 28 0.32
32 34 0.39
33 26 0.30
ACGTcount: A:0.18, C:0.36, G:0.30, T:0.15
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:16205 original size:30 final size:30
Alignment explanation
Indices: 16106--16230 Score: 151
Period size: 30 Copynumber: 4.0 Consensus size: 30
16096 GTGCGTGAGG
* *
16106 CTCGGTCACCATCGGCAATCCCAGGCGGGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGT
* *
16136 GGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 ---CTCGGTCACCATCGGCAAACCCAGAC-GG-GT
16171 CTCGGTCACCATCGGCAAACCCAGACGGGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGT
* *
16201 CTCGGTCACCATCGGCAACCCCCGACGGGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGT
16231 GCCTCGGCAA
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
30 30 0.37
31 2 0.02
32 24 0.29
33 22 0.27
34 2 0.02
35 2 0.02
ACGTcount: A:0.19, C:0.36, G:0.30, T:0.15
Consensus pattern (30 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGT
Found at i:16205 original size:156 final size:157
Alignment explanation
Indices: 15793--16205 Score: 500
Period size: 156 Copynumber: 2.6 Consensus size: 157
15783 AGGCGGGTGG
* * *
15793 CCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAAACCCAGAC-GGTGT
1 CCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATAGGCAAAGCCAGACGGGTGT
*
15857 CTCGGTCACCATC-GCAACCCCCGACGGGTGGCTCGGCAACCCCAGGCCACGGGTGCGGGAGTTC
66 CTCGGTCACCATCGGCAACCCCCGACGGGT-GCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
* *
15921 CGGACAGAGCCGAGAGTTGGGTGCGGGT
130 CGCACAGAACCGAGAGTTGGGTGCGGGT
* * ** * * *** *
15949 CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGG-CAACCCCAGGCCACGGGTG-CGGGGG
1 CCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTC-ACCATAGGCAAAGCCAGACGGGTG
*
16012 CCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC-GGTGCGGGAGTG
65 TCTCGGTCACCATCGGCAACCCCCGACGGGTG-CTCGGCAACCCCAGGCCACGGGTGCGGGAGTG
*
16076 CCGCACAGAACCGAGCGTT-GGTGCGTGAG-
129 CCGCACAGAACCGAGAGTTGGGTGCG-G-GT
* * * *
16105 GCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTG
1 CCTCGGTCACCATCGGCAAACCCAGACGGGT-GCCTCGGTCACCATAGGCAAAGCCAGACGGGTG
* *
16170 TCTCGGTCACCATCGGCAAACCCAGACGGGT-CTCGG
65 TCTCGGTCACCATCGGCAACCCCCGACGGGTGCTCGG
16206 TCACCATCGG
Statistics
Matches: 214, Mismatches: 34, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
155 8 0.04
156 120 0.56
157 52 0.24
158 34 0.16
ACGTcount: A:0.18, C:0.36, G:0.33, T:0.13
Consensus pattern (157 bp):
CCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCGGTCACCATAGGCAAAGCCAGACGGGTGT
CTCGGTCACCATCGGCAACCCCCGACGGGTGCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGCC
GCACAGAACCGAGAGTTGGGTGCGGGT
Found at i:16237 original size:62 final size:63
Alignment explanation
Indices: 16106--16237 Score: 176
Period size: 62 Copynumber: 2.1 Consensus size: 63
16096 GTGCGTGAGG
* * * * *
16106 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-G-CTCGGTCACCATCGGCAAACCCAGACGGGTGC
* *
16171 CTCGGTCACCATCGGCAAACCCAGACGGGT-CTCGGTCACCATCGGCAACCCCCGACGGGTGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGCTCGGTCACCATCGGCAAACCCAGACGGGTGC
16233 CTCGG
1 CTCGG
16238 CAACCCCAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
62 32 0.53
65 28 0.47
ACGTcount: A:0.18, C:0.36, G:0.30, T:0.15
Consensus pattern (63 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGCTCGGTCACCATCGGCAAACCCAGACGGGTGC
Found at i:16300 original size:95 final size:95
Alignment explanation
Indices: 16001--16374 Score: 345
Period size: 95 Copynumber: 4.0 Consensus size: 95
15991 CCCAGGCCAC
16001 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC-G
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
*
16065 GTGCGGGAGTGCCGCACAGAACCGAGCGTT
66 GTGCGGGAGTGCCGCACAGAACCGAGAGTT
* * * * *** *
16095 -GGTGCGTGAGG-CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTC-ACCATTGGCAA
1 GGGTGCG-GGGGCCTCGGTCACCATCGGCAACCCCCGACGGGT-GCCTCGG-CAACCCCAGGCCA
* *** * * * * ***
16157 AGCCAGACGGGTGT-CTCGGTCAC-CATCGGCA-AACC
63 CGGGTG-CGGGAGTGC-C-G-CACAGAACCG-AGAGTT
** * *
16192 CAG-AC--GGGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
*
16254 GTGCGGGAGTGCCGCACAGAGCCGAGAGTT
66 GTGCGGGAGTGCCGCACAGAACCGAGAGTT
* * **
16284 GGGTGCGGGGGCCTCGGTCACCATCGGCAACACCCGACGGGTGCCTCGGCAACCCCAGTCCATTG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
16349 GTGCGGGAGTGCCGCACAGAACCGAG
66 GTGCGGGAGTGCCGCACAGAACCGAG
16375 CGCTGGTGCG
Statistics
Matches: 212, Mismatches: 50, Indels: 35
0.71 0.17 0.12
Matches are distributed among these distances:
91 4 0.02
92 6 0.03
93 42 0.20
94 36 0.17
95 107 0.50
96 7 0.03
97 5 0.02
98 5 0.02
ACGTcount: A:0.18, C:0.34, G:0.35, T:0.13
Consensus pattern (95 bp):
GGGTGCGGGGGCCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
GTGCGGGAGTGCCGCACAGAACCGAGAGTT
Done.