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ZS97RS1
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RS1
RS2
RS3
CRISPR design
PAM
Select a PAM type,there are variety of Cas9's PAM and cpf1's PAM to select
NGG (SpCas9 from Streptococcus pyogenes: 5'-NGG-3')
NRG (SpCas9 from Streptococcus pyogenes: 5'-NRG-3' (R = A, G))
NNAGAAW (StCas9 from Streptococcus thermophilus: 5'-NNAGAAW-3' (W = A, T))
NNNNGMTT (NmCas9 from Neisseria meningitidis: 5'-NNNNGMTT-3' (M = A, C))
NNGRRT (SaCas9 from Staphylococcus aureus: 5'-NNGRRT-'3 (R=A, G))
TTTN (AsCpf1 from Acidaminococcus or LbCpf1 from Lachnospiraceae: 5'-TTTN-3')
TTN (FnCpf1 from Francisella: 5'-TTN-3')
YCN (from Pyrococcus furiosus: 5'-YCN-3' (Y = T, C))
CCW (from Clostridium difficile: 5'-YCN-3' (W = A, T))
YYC (from Bacillus halodurans: 5'-YYC-3' (Y = T, C))
AWG (from Escherichia coli: 5'-AWG-3' (W= A, T))
CC (from Pseudomonas aeruginosa: 5'-CC-3')
MMA (Pyrococcus furiosus: 5'-MMA-3' (M = A, C))
snoRNA promoter
U6 and U3 (default U3) are provides for optional promoters design in plant
U6
U3
RNA Scaffold
Input tracrRNA,for predicting the structue of sgRNA and tracrRNA
Guide Sequence Length
Specify the length of spacer,ranging from 15 to 22(default 20)
20
15
16
17
18
19
21
22
Target Genome
Select a species
Oryza brachyantha (v1.4b)
Oryza glaberrima (AGI1.1)
Oryza indica (ASM465v1)
Oryza indica (MH63RS1)
Oryza indica (MH63RS2)
Oryza indica (ZS97RS1)
Oryza indica (ZS97RS2)
Oryza sativa (RAP-DB)
Oryza sativa(MSU)
Rice kasalath
Locus Tag
gene ID or name
% for some examples
OR
Position
Input position of sequence based on scaffold or chromosome
e.g. Chr3:18864113..18864812
OR
Sequence
Input sequence in fasta format directly
Select a PAM type,there are variety of Cas9's PAM and cpf1's PAM to select