Find common and unique CRISPR guide RNA targets for similar genes or transcripts

Search for common and unique CRISPR guide RNA targets in similar genes or transcripts

5' dinucleotide
Target length
PAM sequence orientation 5' 3'
Allow a mismatch in the first 8 nucleotides? Yes No
PAM sequence NGG (scoring is available*) Your own PAM sequence

*Scoring is available for 20-nt type II sgRNAs. See Doench et al., 2014 for details. High scores may indicate more potent sgRNAs. However, some potent sgRNAs have scores < 0.1 and a number of successful sgRNAs had scores between 0.1 and 0.2. Therefore, potential experimental utility and subsequent experimental verification should guide the choice of sgRNAs.

Off-target analysis parameters:
GT-Scan : No restrictions on PAM sequence or target length. Adjust the target rule on the submission form.
Cas-OFFinder : Length should be 20bp for SpCas9 (PAM = 'NGG'), 18bp for StCas9 (PAM = 'NNAGAAW'), and 24bp for NmCas9 (PAM = 'NNNNGMTT').

Organism (species name)

Type of molecules Gene symbols Ensembl Gene IDs Ensembl Transcripts Refseq sequences*

*Refseq sequences can be from any species

Input gene or transcript identifiers*

*The program supports Ensembl gene and transcript identifiers, gene symbols as well as Refseq cDNA accession numbers (if available). Small number of identifiers (2-3) is most suitable for this application unless similarity is expected to be high.

Demo input

CRISPR MultiTargeter was developed by Sergey Prykhozhij at the IWK Health Centre and Dalhousie University. The design of the logo and the buttons was by Vinothkumar Rajan. The latest update was in in May 2019.