The Streptococcus pyogenes Cas9 (SpCas9) targets 20 nucleotide DNA sequences followed by a 5′-NGG or 5′-NAG PAM sequence. The details of the backbone vectors and other reagents for SpCas9 genome engineering system can be found at the Reagents Page and in the work below:

Cong, L., et al., Multiplex genome engineering using CRISPR/Cas systems. Science, 3 January 2013. (10.1126/science.1231143).

The following tool enables the selection of genomic target sites with minimal likelihood of off-target genome modification.

CRISPR Design Tool (Click Here to Re-direct)

The CRISPR Design Tool allows users to enter a 23-1000bp DNA sequence of interest and will find all SpCas9 target sites within the input sequence. The result will contain a rank ordered list of target sites based on predicted specificity. The algorithm used by this program is based on the specificity analysis performed in Hsu et al., Nature Biotechnology 2013.

Older UCSC Genome Browser tracks

(Important Note: Based on comprehensive analysis of SpCas9 specificity, we have found that the 12bp seed sequence model is not completely predictive of SpCas9 specificity. Therefore we recommend using the new CRISPR Design Tool above. We are working on implementing genomes for other organisms and will have them available soon.)

For application of Cas9 for site-specific genome editing in eukaryotic cells and organisms, we have predicted suitable target sites for the S. pyogenes Cas9. These sites are accessible via the UCSC Genome Browser* for the human, mouse, rat, zebrafish, C. elegans, and D. melanogaster genomes such that the seed sequence for each SpCas9 target site , 5’-NNNNNNNNNNNN-NGG-3’, is unique in the relevant genome.


Homo sapiens (human)

Mus musculus (mouse)

 Rattus norvegicus (rat)

 Danio rerio (zebrafish)

 Drosophila melanogaster (fruit fly)

 Caenorhabditis elegans (roundworm)

Sus scrofa (pig)

Bos taurus (cow)


* These tracks are large and may take up to a minute to load.