CRISPRscan is a novel scoring algorithm from the Giraldez Lab (Yale University) that helps you select the best gRNAs.
Now you can mutate (almost) anything

Genome browser

Tracks for zebrafish, medaka, xenopus, mouse and drosophila are available. Three classes of gRNA sites: (1) High, (2) low scores and (3) sites with off-targets.

View browser tracks

Search for gRNAs on genes

All available gRNA sites predicted and scored with CRISPRscan within coding-sequence of protein-coding genes.

Target protein-coding genes

Predict gRNAs on your sequences

Submit your sequence to search gRNAs. Select your genome to predict off-targets.

Predict gRNAs

Select gRNAs

All Cas9 gRNAs are scored with CRISPRscan model. Select gRNAs with highest score to increase your chance to get a mutant.

Multiple species

CRISPRscan includes predictions for zebrafish, Xenopus, human, mouse, Drosophila and more...

Export gRNAs

Refine your choice of gRNAs after exporting CRISPRscan predictions on your computer.


Whole genomes are searched for off-targets with up to 4 mismatches. Multiple scores and rules are available.

Off-target rules

Protein domain

Protein domain annotations from Pfam, SMART, PROSITE, HMM-Panther, HAMAP etc are included in CRISPRscan.

gRNA generation

Order the CRISPRscan provided oligo and generate your ready-to-inject sgRNA.