June 2017: CRISPOR Batch for lentiviral screens, saturation-mutagenesis and Genbank export now in the beta of Crispor V4.3.
CRISPOR is a program that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system.

CRISPOR v4.0 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.

Version V4.2, Apr 2017: Genome variants, Cpf1, Off-target primers, microhomology, Genbank-export, Sat. mutagenesis and more
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: pre-calculated exonic guides for this species are on the UCSC Genome Browser.
We have 226 genomes, but not the one you need? Send its FASTA/GFF URL to CRISPOR support
Step 3
Select a Protospacer Adjacent Motif (PAM)
Version 4.2, 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.