Eukaryotic Pathogen CRISPR guide RNA/DNA Design Tool

with (1) custom genome upload, (2) off-target analysis, (3) on-targets searching (for targeting gene families), (4) efficiency/activity prediction, (5) assisted oligo repair template design , (6) gRNA transcription problem identification, (7) flanking microhomology searching (for predicting deletions)

** Gene Tagging ** Batch Mode

upload and process multiple sequences in one run

if you are processing one gene, please use this link

automatically identify gRNA and corresponding HDR template to insert tags

tag inserts after start codons and before stop codons

Please flank your ORF with UTR sequence, and specify length of UTRs

Job Name:

RNA/DNA guided nuclease selection:(?)

choose one to automatically configure gRNA/gDNA and PAM settings for each nuclease

Additional option settings: (click to expand a category)

Batch process parameters (please click to review!)

Only 2 gRNAs will be picked for each input sequence.
One for 5' tagging, the other for 3' tagging
The successful gRNAs should pass the below filter for quality:

minimum gRNA efficay score:  

minimum gRNA GC%:  

maximum gRNA GC%:  

Each sequence can be in the format of 5'UTR-ORF-3'UTR,
Please specify UTR length in your sequence

5' UTR length: (50-90bp recommended)

3' UTR length: (50-90bp recommended)

HDR oligo template parameters (for tagging)

For each gRNA, a HDR oligo repair template will be provided,
for the insertion of a custom sequence (tag) into your gene.
The insertion sequence would be arranged in an in-frame fashion
(assuming 1st reading frame in your input sequence,
e.g. first 3 nt is a codon and so on so forth)

homology arm length:(?)     


gRNA search parameters

gRNA length:  

PAM motif(s):
(use comma to separate multiple PAM motifs
use IUPAC code for degenerate base)

on-target search parameters

(Default settings
recommended for most users)

homology arm length:

off-target search parameters

(Default settings
recommended for most users)

maximum number
of mismatches:

off-target PAM motif(s)(?):
(comma separated if more than one,
use IUPAC code for degenerate base)

Genome (expand a category and choose one):

genome naming paradigm:
specie strain database-version


or upload your fasta file here: 

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