Simple CRISPR guide RNA target search in input sequence(s)

5' dinucleotide
Target length
PAM sequence orientation 5' 3'
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').

Type of gRNA design Single double-strand cut Two single-strand nicks by Nickase

When binding a guide RNA, wild-type Cas9 produces a single double-strand cut, whereas D10A Cas9 mutant (nickase) generates single-stranded nicks in DNA and therefore requires two guide RNAs to induce a cut in DNA.

Please select the spacing between two gRNA target sites from 0 to 20.

Minimal spacer length Maximum spacer length

Please enter your sequence(s) in the text box below

Input sequence(s)*

*Please enter one or more sequences in FASTA format, each smaller than 50 kb and having unique names.
Search of target sites will be performed independently in each sequence.

OR Upload a file with sequences:

Demo for sequence input

OR enter identifiers of genes or transcripts to run the program on.

Organism (species name)
Type of molecules Sequence input 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).

Demo for identifier 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 May 2019.