Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009481.1 Hibiscus syriacus cultivar Beakdansim tig00114484_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: 6916
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Found at i:2818 original size:32 final size:32
Alignment explanation
Indices: 2759--2889 Score: 169
Period size: 32 Copynumber: 4.2 Consensus size: 32
2749 CCTGGGGTTG
* *
2759 CCGAGGCACCCGTC-GGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
2790 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
2822 CCGAGACACCCGTCTGGCTTTGCCAATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* * *
2854 CCGAGGCCACCC-CCT-GGATTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
2885 CCGAG
1 CCGAG
2890 CCTCACGCAC
Statistics
Matches: 89, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
30 1 0.01
31 30 0.34
32 52 0.58
33 6 0.07
ACGTcount: A:0.16, C:0.31, G:0.34, T:0.18
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Found at i:2876 original size:63 final size:63
Alignment explanation
Indices: 2759--2889 Score: 167
Period size: 63 Copynumber: 2.1 Consensus size: 63
2749 CCTGGGGTTG
* * * * *
2759 CCGAGGCACCCGTCGGGGTTGCCGATGGTGACCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCGGCGTTGCCAATGGTGACCGAGACACCCGCCTGGGATTGCCGATGGTGA
* *
2822 CCGAGACACCCGTCTGGCTTTGCCAATGGTGACCGAGGCCACCC-CCT-GGATTGCCGATGGTGA
1 CCGAGACACCCGTC-GGCGTTGCCAATGGTGACCGA-GACACCCGCCTGGGATTGCCGATGGTGA
2885 CCGAG
1 CCGAG
2890 CCTCACGCAC
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 33 0.56
64 20 0.34
65 6 0.10
ACGTcount: A:0.16, C:0.31, G:0.34, T:0.18
Consensus pattern (63 bp):
CCGAGACACCCGTCGGCGTTGCCAATGGTGACCGAGACACCCGCCTGGGATTGCCGATGGTGA
Found at i:3051 original size:59 final size:61
Alignment explanation
Indices: 2924--3053 Score: 228
Period size: 59 Copynumber: 2.1 Consensus size: 61
2914 GTGCGGCACT
*
2924 CCCGCACCCGTGGCCTGGGTTGCCGAGGCACCCGTCGGGGGTTGCCGATGGTGACCGAGGCC
1 CCCGCACCCGTGGCCTGGGTTGCCGAGGCACCCG-CGGGGGTTGCCGATGGTGACCGAGGAC
2986 CCCGCACCCGTGGCCTGGGTTGCCGAGGCA-CC-CGGGGGTTGCCGATGGTGACCGAGGAC
1 CCCGCACCCGTGGCCTGGGTTGCCGAGGCACCCGCGGGGGTTGCCGATGGTGACCGAGGAC
3045 CCCGCACCC
1 CCCGCACCC
3054 AACTCTCGGC
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
59 35 0.52
61 2 0.03
62 30 0.45
ACGTcount: A:0.11, C:0.38, G:0.38, T:0.13
Consensus pattern (61 bp):
CCCGCACCCGTGGCCTGGGTTGCCGAGGCACCCGCGGGGGTTGCCGATGGTGACCGAGGAC
Found at i:3158 original size:32 final size:32
Alignment explanation
Indices: 3099--3230 Score: 205
Period size: 32 Copynumber: 4.2 Consensus size: 32
3089 GCCTGGGTTG
* *
3099 CCGAGCCACCCGTC-GGGGTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
3130 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
3162 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
* *
3194 CCGAGGCCACCCGCCTGGG-TTGCCGATGGTGA
1 CCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
3226 CCGAG
1 CCGAG
3231 CCTCACGCAC
Statistics
Matches: 95, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
31 14 0.15
32 69 0.73
33 12 0.13
ACGTcount: A:0.14, C:0.31, G:0.36, T:0.18
Consensus pattern (32 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGA
Found at i:3217 original size:64 final size:65
Alignment explanation
Indices: 3099--3364 Score: 208
Period size: 64 Copynumber: 4.0 Consensus size: 65
3089 GCCTGGGTTG
* * * * *
3099 CCGAGCCACCCGTC-GGGGTTGCCGATGGTGACCGA-GACACCCGTCTGGGTTTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
3162 CCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGCCACCCGCCTGGG-TTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
* * **** *** *
3226 CCGAGCCTCACGCACCAACG-CTCGG-TT-CTG-TGCG-GCACTCCCTCACCAATGGCCTGGGGT
1 CCGAG----A--CACC--CGTCTGGGTTTGCCGATG-GTG-A--CCGAGGCCACCCGCCTGGGAT
3286 TGCCGATGGTGA
54 TGCCGATGGTGA
* *
3298 CCGAGACA-CCGTATGGTTTTGCCGATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
1 CCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
3362 CCG
1 CCG
3365 GGGCTCACGC
Statistics
Matches: 158, Mismatches: 25, Indels: 39
0.71 0.11 0.18
Matches are distributed among these distances:
63 15 0.09
64 68 0.43
65 15 0.09
66 6 0.04
67 3 0.02
68 5 0.03
69 4 0.03
70 6 0.04
71 16 0.10
72 20 0.13
ACGTcount: A:0.15, C:0.32, G:0.34, T:0.19
Consensus pattern (65 bp):
CCGAGACACCCGTCTGGGTTTGCCGATGGTGACCGAGGCCACCCGCCTGGGATTGCCGATGGTGA
Found at i:3358 original size:33 final size:31
Alignment explanation
Indices: 3277--3364 Score: 104
Period size: 33 Copynumber: 2.8 Consensus size: 31
3267 CTCACCAATG
*
3277 GCCTGGGGTTGCCGATGGTGACCGAGACACC
1 GCCTGGGATTGCCGATGGTGACCGAGACACC
** ** *
3308 GTATGGTTTTGCCGATGGTGACCGAGGCCACCC
1 GCCTGGGATTGCCGATGGTGACCGA-GACA-CC
3341 GCCTGGGATTGCCGATGGTGACCG
1 GCCTGGGATTGCCGATGGTGACCG
3365 GGGCTCACGC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
31 21 0.46
32 3 0.07
33 22 0.48
ACGTcount: A:0.15, C:0.27, G:0.38, T:0.20
Consensus pattern (31 bp):
GCCTGGGATTGCCGATGGTGACCGAGACACC
Done.