Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009497.1 Hibiscus syriacus cultivar Beakdansim tig00114728_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: 7897
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.21
Found at i:5519 original size:32 final size:32
Alignment explanation
Indices: 5480--5567 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
5470 GCGTGAGCCC
*
5480 CGGTCACCATC-GCAATCCCAGGCGGGTGGCCT
1 CGGTCACCATCGGCAAACCCAGGCGGGT-GCCT
* ** *
5512 CGGTCACCATCGGCAAAACCATACGGGTGTCT
1 CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
*
5544 CGGTCACCATCGGCAACCCCAGGC
1 CGGTCACCATCGGCAAACCCAGGC
5568 CATTGGTGAG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
32 34 0.74
33 12 0.26
ACGTcount: A:0.20, C:0.38, G:0.27, T:0.15
Consensus pattern (32 bp):
CGGTCACCATCGGCAAACCCAGGCGGGTGCCT
Found at i:5653 original size:32 final size:32
Alignment explanation
Indices: 5612--5743 Score: 196
Period size: 32 Copynumber: 4.2 Consensus size: 32
5602 GTGCGTGAGG
* *
5612 CTCGGTCACCATCGGC-AACCCAGGCGGGTGGC
1 CTCGGTCACCATCGGCAAACCCAGACGGGT-GT
5644 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
5676 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
* * *
5708 CTCGGTCACCATC-GCAACCCCCGACGGGTGG
1 CTCGGTCACCATCGGCAAACCCAGACGGGTGT
5739 CTCGG
1 CTCGG
5744 CAACCCCAGG
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
31 20 0.21
32 62 0.66
33 12 0.13
ACGTcount: A:0.18, C:0.37, G:0.30, T:0.14
Consensus pattern (32 bp):
CTCGGTCACCATCGGCAAACCCAGACGGGTGT
Found at i:5885 original size:61 final size:61
Alignment explanation
Indices: 5790--5920 Score: 237
Period size: 61 Copynumber: 2.1 Consensus size: 61
5780 GCCGAGAGTT
*
5790 GGGTGCGGGTCCTCGGTCACCATCGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGCCTCGGTCACCATCGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
5851 GGGTGCGGGGCCTC-GTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
1 GGGTGCGGGGCCTCGGTCACCATC-GCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
5912 GGGTGCGGG
1 GGGTGCGGG
5921 AGTGCCGCAC
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
60 9 0.13
61 59 0.87
ACGTcount: A:0.14, C:0.40, G:0.35, T:0.11
Consensus pattern (61 bp):
GGGTGCGGGGCCTCGGTCACCATCGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCAC
Found at i:6052 original size:31 final size:32
Alignment explanation
Indices: 5958--6086 Score: 170
Period size: 32 Copynumber: 4.0 Consensus size: 32
5948 CGTGAGGCTC
* *
5958 GTCACCATCGGCAATCCCAGGCGGGTGGCCTCG
1 GTCACCATCGGCAAACCCAGACGGGT-GCCTCG
* * *
5991 GTCACCATTGGCAAAGCCAGACGGGTGTCTCG
1 GTCACCATCGGCAAACCCAGACGGGTGCCTCG
*
6023 GTCACCATCGGCAAACCCAGAC-GGTGTCTCG
1 GTCACCATCGGCAAACCCAGACGGGTGCCTCG
* *
6054 GTCACCATCGGCAACCCCCGACGGGTGCCTCG
1 GTCACCATCGGCAAACCCAGACGGGTGCCTCG
6086 G
1 G
6087 CAACCCCAGG
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
31 29 0.34
32 34 0.40
33 22 0.26
ACGTcount: A:0.19, C:0.36, G:0.30, T:0.16
Consensus pattern (32 bp):
GTCACCATCGGCAAACCCAGACGGGTGCCTCG
Found at i:6077 original size:63 final size:65
Alignment explanation
Indices: 5958--6086 Score: 172
Period size: 63 Copynumber: 2.0 Consensus size: 65
5948 CGTGAGGCTC
* * * * *
5958 GTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATTGGCAAAGCCAGACGGGTGTCTCG
1 GTCACCATCGGCAAACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCG
* * *
6023 GTCACCATCGGCAAACCCAGAC-GGT-GTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCG
1 GTCACCATCGGCAAACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCG
6086 G
1 G
6087 CAACCCCAGG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 33 0.59
64 3 0.05
65 20 0.36
ACGTcount: A:0.19, C:0.36, G:0.30, T:0.16
Consensus pattern (65 bp):
GTCACCATCGGCAAACCCAGACGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGCCTCG
Found at i:6211 original size:91 final size:95
Alignment explanation
Indices: 5851--6231 Score: 281
Period size: 95 Copynumber: 4.1 Consensus size: 95
5841 CCCAGGCCAC
*
5851 GGGTGC-GGGGCCTC-GTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCACCGACGGGTGCCTCGGCAACCCCAGGCCACGG
*
5914 GTGCGGGAGTGCCGCACAGAACCGAGCG-T
66 GTGCGGGAGTGCCGCACAGAACCGAGAGCT
* * * * *** *
5943 TGGTGCGTGAGG-CTC-GTCACCATCGGCAATCC-CAGGCGGGTGGCCTCGGTC-ACCATTGGCA
1 GGGTGCG-GGGGCCTCGGTCACCATCGGCAA-CCACCGACGGGT-GCCTCGG-CAACCCCAGGCC
* *** * * * * * *
6004 AAGCCAGACGGGTGT-CTCGGTCAC-CATCGGCA-AACC
62 ACGGGTG-CGGGAGTGC-C-G-CACAGAACCG-AGAGCT
** * * * *
6040 CAG-AC-GGTGTCTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCACCGACGGGTGCCTCGGCAACCCCAGGCCACGG
* *
6103 GTGCGGGAGTGCCGCACAGAGCCGAGAGTT
66 GTGCGGGAGTGCCGCACAGAACCGAGAGCT
* **
6133 GGGTGCGGGGGCCTCGGTCACCATCGGCAA-CACC-AC-GGTGCCTCGGCAACCCC-GTCCATTG
1 GGGTGCGGGGGCCTCGGTCACCATCGGCAACCACCGACGGGTGCCTCGGCAACCCCAGGCCACGG
*
6194 GTGCGGGAGTGCCGCACAGAACCGAGCGCT
66 GTGCGGGAGTGCCGCACAGAACCGAGAGCT
6224 GGGTGCGG
1 GGGTGCGG
6232 CAGCCTCGCA
Statistics
Matches: 216, Mismatches: 53, Indels: 41
0.70 0.17 0.13
Matches are distributed among these distances:
91 40 0.19
92 26 0.12
93 32 0.15
94 36 0.17
95 51 0.24
96 26 0.12
97 5 0.02
ACGTcount: A:0.17, C:0.34, G:0.35, T:0.13
Consensus pattern (95 bp):
GGGTGCGGGGGCCTCGGTCACCATCGGCAACCACCGACGGGTGCCTCGGCAACCCCAGGCCACGG
GTGCGGGAGTGCCGCACAGAACCGAGAGCT
Found at i:6238 original size:91 final size:95
Alignment explanation
Indices: 6050--6239 Score: 271
Period size: 91 Copynumber: 2.0 Consensus size: 95
6040 CAGACGGTGT
*
6050 CTCGGTCACCATCGGCAACCCCCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
1 CTCGGTCACCATCGGCAACCACCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
* * **
6115 CGCACAGAGCCGAGAGTTGGGTGCGGGGGC
66 CGCACAGAACCGAGAGCTGGGTGCGGCAGC
* **
6145 CTCGGTCACCATCGGCAA-CACC-AC-GGTGCCTCGGCAACCCC-GTCCATTGGTGCGGGAGTGC
1 CTCGGTCACCATCGGCAACCACCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
*
6206 CGCACAGAACCGAGCGCTGGGTGCGGCAGC
66 CGCACAGAACCGAGAGCTGGGTGCGGCAGC
6236 CTCG
1 CTCG
6240 CACAGCGTCG
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
91 46 0.53
92 17 0.20
93 2 0.02
94 3 0.03
95 18 0.21
ACGTcount: A:0.16, C:0.36, G:0.36, T:0.12
Consensus pattern (95 bp):
CTCGGTCACCATCGGCAACCACCGACGGGTGCCTCGGCAACCCCAGGCCACGGGTGCGGGAGTGC
CGCACAGAACCGAGAGCTGGGTGCGGCAGC
Done.