Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007685.1 Hibiscus syriacus cultivar Beakdansim tig00029187_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: 26427
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.21
Found at i:5969 original size:31 final size:32
Alignment explanation
Indices: 5923--6009 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 32
5913 GCCCCCGTGT
* *
5923 GCGTGCGCCTC-GTCACCATCGGTAATCCAAG
1 GCGTGCGCCTCGGTCACCATCGGCAAACCAAG
*
5954 GCGTG-GCCTCGGTCACCATCGGCAAACCCAG
1 GCGTGCGCCTCGGTCACCATCGGCAAACCAAG
* * *
5985 ACG-GTGTCTCGGTCACCATCGGCAA
1 GCGTGCGCCTCGGTCACCATCGGCAA
6010 CCCCGGCCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 6 0.12
31 43 0.88
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.17
Consensus pattern (32 bp):
GCGTGCGCCTCGGTCACCATCGGCAAACCAAG
Found at i:6139 original size:167 final size:169
Alignment explanation
Indices: 5792--6366 Score: 977
Period size: 167 Copynumber: 3.4 Consensus size: 169
5782 ACGTGTGCGT
**
5792 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
5857 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGG-CCCCGTG
* *
5922 TGCGTGCGCCTC-GTCACCATCGGTAATCCAAGGC--GTG
130 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
5959 GCCTCGGTCACCATCGGCAAACCCAGAC-GGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
6022 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
6087 GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
131 GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
6126 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATC-GCAACCCC-GGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* * *
6189 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGGCCGCTTGT
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
*
6254 GCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTTG
131 GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGG-TG
*
6294 GCCTCGGTCACCATCGGCAAACCC-GACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
6358 GTGCGGGAG
66 GTGCGGGAG
6367 CCTCGGTCAC
Statistics
Matches: 388, Mismatches: 13, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
164 18 0.05
165 84 0.22
166 27 0.07
167 191 0.49
168 51 0.13
169 17 0.04
ACGTcount: A:0.17, C:0.34, G:0.33, T:0.17
Consensus pattern (169 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:6169 original size:32 final size:33
Alignment explanation
Indices: 6093--6173 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
6083 GTGTGCGTGA
* *
6093 GCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
6126 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
6158 GTCTCGGTCACCATCG
1 GCCTCGGTCACCATCG
6174 CAACCCCGGC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 15 0.34
33 29 0.66
ACGTcount: A:0.19, C:0.36, G:0.30, T:0.16
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
Found at i:6334 original size:31 final size:32
Alignment explanation
Indices: 6260--6448 Score: 150
Period size: 31 Copynumber: 5.6 Consensus size: 32
6250 TTGTGCGTGA
* *
6260 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTT
1 GCCTCGGTCACCATCGGCAAACCCAGACGGG-T
6293 GGCCTCGGTCACCATCGGCAAACCC-GACGGGT
1 -GCCTCGGTCACCATCGGCAAACCCAGACGGGT
* * * * *
6325 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGGA
1 GCCTCGGTCACCATCGGCAA--AC---CCA---G-ACGGGT
** *
6366 GCCTCGGTCACCATCGGCAGTCCCAGGCGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGT
6398 GGCCTC-GTCACCATCGGCAAA-CCAGACGGGT
1 -GCCTCGGTCACCATCGGCAAACCCAGACGGGT
*
6429 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
6449 CCCCGGGCCA
Statistics
Matches: 127, Mismatches: 16, Indels: 27
0.75 0.09 0.16
Matches are distributed among these distances:
30 4 0.03
31 41 0.32
32 19 0.15
33 12 0.09
34 23 0.18
36 5 0.04
39 1 0.01
40 1 0.01
41 21 0.17
ACGTcount: A:0.17, C:0.35, G:0.31, T:0.16
Consensus pattern (32 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGT
Found at i:6442 original size:104 final size:106
Alignment explanation
Indices: 6252--6470 Score: 388
Period size: 104 Copynumber: 2.1 Consensus size: 106
6242 CAGGCCGCTT
*
6252 GTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTTGGCCTCGGTCACCATCGGCAAACC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTTGGCCTCGGTCACCATCGGCAAACC
* *
6317 CGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
*
6358 GTGCGGGAGCCTCGGTCACCATCGGCAGTCCCAGGCGGG-TGGCCTC-GTCACCATCGGCAAACC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTTGGCCTCGGTCACCATCGGCAAACC
6421 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
6462 GTGCGGGAG
1 GTGCGGGAG
6471 TGCCGCACAG
Statistics
Matches: 109, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
104 65 0.60
105 7 0.06
106 37 0.34
ACGTcount: A:0.16, C:0.34, G:0.33, T:0.16
Consensus pattern (106 bp):
GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTTGGCCTCGGTCACCATCGGCAAACC
AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
Found at i:19504 original size:32 final size:33
Alignment explanation
Indices: 19428--19512 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
19418 GTGTGCGTGC
* * *
19428 GCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
19461 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
19493 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
19513 CCCCGGCCAT
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:0.20, C:0.34, G:0.29, T:0.16
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
Found at i:19589 original size:169 final size:169
Alignment explanation
Indices: 19292--19871 Score: 1038
Period size: 169 Copynumber: 3.4 Consensus size: 169
19282 ACGTGTGCGT
**
19292 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
19357 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
* *
19422 GCGTGCGCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
131 GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
19461 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
19525 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGG-CCCCGTG
19590 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
130 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
19630 GCCTCGGTCACCATCGGCAAACCCAGAC-GGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* * *
19694 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGGCCGCTTGT
66 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
*
19759 GCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
131 GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
19798 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
19863 GTGCGGGAG
66 GTGCGGGAG
19872 CCTCGGTCAC
Statistics
Matches: 395, Mismatches: 13, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
168 162 0.41
169 233 0.59
ACGTcount: A:0.17, C:0.33, G:0.33, T:0.16
Consensus pattern (169 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
GCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:19670 original size:31 final size:33
Alignment explanation
Indices: 19597--19680 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
19587 GTGTGCGTGA
* *
19597 GCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
19630 GCCTCGGTCACCATCGGCAAACCCAGAC-GGT-
1 GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
*
19661 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
19681 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 3 0.06
33 25 0.53
ACGTcount: A:0.20, C:0.36, G:0.29, T:0.15
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCAAGACGGGTG
Found at i:19807 original size:33 final size:33
Alignment explanation
Indices: 19765--19955 Score: 197
Period size: 33 Copynumber: 5.6 Consensus size: 33
19755 TTGTGCGTGA
*
19765 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
19798 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
* * * * *
19830 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG
**
19870 AGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
19904 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
19936 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
19956 CCCCGGGCCA
Statistics
Matches: 131, Mismatches: 18, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
32 41 0.31
33 60 0.46
34 2 0.02
35 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 1 0.01
41 22 0.17
ACGTcount: A:0.17, C:0.36, G:0.31, T:0.16
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
Found at i:19839 original size:65 final size:66
Alignment explanation
Indices: 19765--19955 Score: 197
Period size: 65 Copynumber: 2.8 Consensus size: 66
19755 TTGTGCGTGA
*
19765 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
19830 -
66 G
* * * * * **
19830 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGGGAGCCTCGGTCACCATCGGCAGTCCC
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG-GCCTCGGTCACCATCGGCAAACCC
*
19895 AGGCGGGTG
58 AGACGGGTG
* *
19904 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAA
19956 CCCCGGGCCA
Statistics
Matches: 101, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
65 41 0.41
66 1 0.01
67 1 0.01
68 1 0.01
69 1 0.01
70 1 0.01
71 1 0.01
72 2 0.02
73 30 0.30
74 22 0.22
ACGTcount: A:0.17, C:0.36, G:0.31, T:0.16
Consensus pattern (66 bp):
GCCTCGGTCACCATCGGCAAACCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGT
G
Found at i:19882 original size:106 final size:106
Alignment explanation
Indices: 19757--19977 Score: 415
Period size: 106 Copynumber: 2.1 Consensus size: 106
19747 CAGGCCGCTT
*
19757 GTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
*
19822 AGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
*
19863 GTGCGGGAGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
19928 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
66 AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
19969 GTGCGGGAG
1 GTGCGGGAG
19978 TGCCGCACAG
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 112 1.00
ACGTcount: A:0.16, C:0.34, G:0.33, T:0.16
Consensus pattern (106 bp):
GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
AGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
Found at i:20359 original size:11 final size:11
Alignment explanation
Indices: 20345--20376 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
20335 TCCCGGTGGT
20345 GCTCCGGCGAC
1 GCTCCGGCGAC
*
20356 GCTCCGGCGAT
1 GCTCCGGCGAC
20367 GCTCCGGCGA
1 GCTCCGGCGA
20377 GACATTATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.38, T:0.12
Consensus pattern (11 bp):
GCTCCGGCGAC
Done.