Mar 2017: lentiviral saturation-mutagenesis assistant and Genbank sequence export now in the beta of Crispor V4.2. Do not hesitate to contact us for feedback or bugs reports.
Apr 2017: the search was down for one day on Apr 21. It is back up now, all submitted jobs should be complete now.
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.

New version V4, Mar 2017: Support for genome variants, Cpf1, Off-target primers, microhomology. Full list of changes
Step 1
Sequence name (optional):
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
Step 2
Select a genome

Note: we have pre-calculated all exonic guides for this species. Have a look at the UCSC Genome Browser.
Missing a genome? Send us email
Step 3
Select a Protospacer Adjacent Motif (PAM)
Version 4.0, Feedback: email - Downloads/local installation
CRISPR/Cas9 Guide Designer for chordate vertebrate ecdysozoans lophotrochozoans protostomes spongi corals plants butterflies metazoans genomes fruitflies insects nematodes mammals.