Have a look at the first version of the brand new manual for CRISPOR.
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.

New version V4.3, Oct 2017: Lentiviral screens, Variants, Cpf1, Off-target primers, microhomology, Genbank-export, Sat. mutagenesis . Full list of changes
Step 1
Planning a lentiviral gene knockout screen? Use CRISPOR Batch
Sequence name (optional):
Enter a single genomic sequence, < 2000 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 268 genomes, but not the one you need? Send its FASTA/GFF URL to CRISPOR support
Step 3
Select a Protospacer Adjacent Motif (PAM)
Version 4.3, 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.