Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008962.1 Hibiscus syriacus cultivar Beakdansim tig00112298_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: 7648
ACGTcount: A:0.22, C:0.27, G:0.31, T:0.21
Found at i:5788 original size:33 final size:32
Alignment explanation
Indices: 5751--5835 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 32
5741 GTGTGCGTGC
* * *
5751 GCCTCGGTCACCATCGGTAATCCAAGGCGGGT
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGT
* *
5783 GGCCTCGGTCACCATCGACAAACCCAGACGGGT
1 -GCCTCGGTCACCATCGGCAAACCAAGACGGGT
*
5816 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
5836 CCCCGGCCAT
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:5930 original size:169 final size:168
Alignment explanation
Indices: 5616--6186 Score: 965
Period size: 169 Copynumber: 3.4 Consensus size: 168
5606 ACGTGTGCGT
**
5616 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
*
5681 GT--GGGAGTGCCGCACAGAACGAGCGTTGGTGCGGGAGCCTCGGTTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGACCGAGCGTTGGTGCGGGAGCCTCGG-TCACCATCAGGCCCCCGTG
* *
5744 TGCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
130 TGCGTGAGCCTCGGTCACCATCGGCAATCC-AGGCGGGTG
*
5784 GCCTCGGTCACCATCGACAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
*
5848 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAG-ACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
*
5913 TGCGTGAGCCTCGGTCACCATCGGCAATCCTGGGCGGGTG
130 TGCGTGAGCCTCGGTCACCATCGGCAATCC-AGGCGGGTG
5953 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAA-CCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
6017 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG--CCCTTG
66 GTGCGGGAGTGCCGCACAG-ACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
6080 TGCGTGAGCCTCGGTCACCATCGGCAATCCAGGCGGGTG
130 TGCGTGAGCCTCGGTCACCATCGGCAATCCAGGCGGGTG
6119 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
6184 GTG
66 GTG
6187 GGGCCTCGGG
Statistics
Matches: 383, Mismatches: 15, Indels: 11
0.94 0.04 0.03
Matches are distributed among these distances:
166 60 0.16
167 60 0.16
168 56 0.15
169 183 0.48
170 24 0.06
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.17
Consensus pattern (168 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTGCCGCACAGACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTGT
GCGTGAGCCTCGGTCACCATCGGCAATCCAGGCGGGTG
Found at i:5996 original size:32 final size:33
Alignment explanation
Indices: 5920--6004 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
5910 GTGTGCGTGA
* ** *
5920 GCCTCGGTCACCATCGGCAATCCTGGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
5953 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
*
5985 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
6005 CCCGGGCCAT
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:6128 original size:32 final size:31
Alignment explanation
Indices: 6087--6289 Score: 137
Period size: 32 Copynumber: 6.7 Consensus size: 31
6077 TTGTGCGTGA
* *
6087 GCCTCGGTCACCATCGGCAATCCAGGCGGGT
1 GCCTCGGTCACCATCGGCAACCCAGACGGGT
6118 GGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 -GCCTCGGTCACCATCGGC-AACCCAGACGGGT
*
6151 GTCTCGGTCACCATCGGCAACCC---C-GG-
1 GCCTCGGTCACCATCGGCAACCCAGACGGGT
* ** * *
6177 GCCATTGGTGGGGCC-TCGG------GGA--GGA
1 GCC-TCGGT--CACCATCGGCAACCCAGACGGGT
* *
6202 GCCTCGGTCACCATCGGCAGTCCCAGGCGGGT
1 GCCTCGGTCACCATCGGCA-ACCCAGACGGGT
6234 GGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 -GCCTCGGTCACCATCGGC-AACCCAGACGGGT
*
6267 GTCTCGGTCACCATCGGCAACCC
1 GCCTCGGTCACCATCGGCAACCC
6290 GGGCCATTGG
Statistics
Matches: 135, Mismatches: 16, Indels: 41
0.70 0.08 0.21
Matches are distributed among these distances:
22 2 0.01
23 4 0.03
24 6 0.04
25 3 0.02
26 2 0.01
27 6 0.04
28 5 0.04
29 2 0.01
30 1 0.01
31 10 0.07
32 54 0.40
33 39 0.29
34 1 0.01
ACGTcount: A:0.17, C:0.36, G:0.33, T:0.15
Consensus pattern (31 bp):
GCCTCGGTCACCATCGGCAACCCAGACGGGT
Found at i:6244 original size:33 final size:32
Alignment explanation
Indices: 6202--6286 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 32
6192 TCGGGGAGGA
** *
6202 GCCTCGGTCACCATCGGCAGTCCCAGGCGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGT
6234 GGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 -GCCTCGGTCACCATCGGCAAACCCAGACGGGT
*
6267 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
6287 CCCGGGCCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
32 19 0.40
33 29 0.60
ACGTcount: A:0.18, C:0.36, G:0.31, T:0.15
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGT
Found at i:6288 original size:116 final size:114
Alignment explanation
Indices: 6085--6301 Score: 407
Period size: 116 Copynumber: 1.9 Consensus size: 114
6075 CCTTGTGCGT
6085 GAGCCTCGGTCACCATCGGCAATCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGG
1 GAGCCTCGGTCACCATCGGCAATCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGG
6150 TGTCTCGGTCACCATCGGCAACCCCGGGCCATTGGTGGGGCCTCGGGGAG
66 TGTCTCGGTCACCATCGGCAA-CCCGGGCCATTGGTGGGGCCTCGGGGAG
*
6200 GAGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGG
1 GAGCCTCGGTCACCATCGGCAAT-CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGG
6265 GTGTCTCGGTCACCATCGGCAACCCGGGCCATTGGTG
65 GTGTCTCGGTCACCATCGGCAACCCGGGCCATTGGTG
6302 CGGGAGTGCC
Statistics
Matches: 100, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
115 37 0.37
116 63 0.63
ACGTcount: A:0.17, C:0.35, G:0.34, T:0.15
Consensus pattern (114 bp):
GAGCCTCGGTCACCATCGGCAATCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGG
TGTCTCGGTCACCATCGGCAACCCGGGCCATTGGTGGGGCCTCGGGGAG
Found at i:6693 original size:10 final size:10
Alignment explanation
Indices: 6667--6698 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
6657 TCCCGGTGGT
6667 GCTCCGGCGA
1 GCTCCGGCGA
6677 CGCTCCGGCGA
1 -GCTCCGGCGA
6688 GCTCCGGCGA
1 GCTCCGGCGA
6698 G
1 G
6699 ACATTATCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.09, C:0.41, G:0.41, T:0.09
Consensus pattern (10 bp):
GCTCCGGCGA
Done.