Christmas 2016: many new features in our new beta of Crispor V4. Thanks for the many suggestions! Please send us email if you find bugs in the new version.
CRISPOR is a program that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system.

CRISPOR v3.0 uses the BWA algorithm to identify guide RNA sequences for CRISPR mediated genome editing.
It searches for off-target sites (with and without mismatches), shows them in a table and annotates them with flanking genes.
For more information on principles of CRISPR-mediated genome editing, check the Addgene CRISPR guide.
Step 1
Enter a single genomic sequence, < 1000 bp, typically an exon
Clear Box - Reset to default
Text case is preserved, e.g. you can mark ATGs with lowercase.
Instead of a sequence, you can paste a chromosome range, e.g. chr1:11908-12378. Positions to avoid can be marked with N, e.g. for SNPs.
Step 2
Select a genome
Note: we have pre-calculated all human exon guides.

Missing a genome? Send us email
Step 3
Select a Protospacer Adjacent Motif (PAM)
Version 3.1, Feedback: By email or in the forum. Downloads and local install
CRISPR/Cas9 Guide Designer for chordate vertebrate ecdysozoans lophotrochozoans protostomes spongi corals plants butterflies metazoans genomes fruitflies insects nematodes mammals.