A bulge-allowed quick guide-RNA designer for CRISPR/Cas derived RGENs.

Cas-Designer provides all possible RGEN targets in the given input sequence (e.g. exon), with the useful information including potential off-target numbers within 2nt mismatches and optional 3nt bulge via Cas-OFFinder, and out-of-frame scores via Microhomology-predictor. If you want to search with more mismatch numbers or bigger bulge size, then you can download and use a standalone edition of Cas-Designer.

PAM Type

CRISPR/Cas-derived RNA-guided Endonucleases (RGENs)

Target Genome

Organism Type



Send request for a new organism.

Please specify how to download the reference genome 2bit or FASTA files of the organism.

Target Sequence

Insert any sequence(s) where you want to search for RGEN targets (raw sequence or FASTA format, maximum 1000 chars):

Or, upload a FASTA-formatted file containing target sequence(s) (maximum 1 KiB):

crRNA length
(length of target without PAM)

(Optional) Target searching range (e.g. Exon)[?]:



2017.12.06. Due to the overload of server, bulge is limited to 1.