CRISPR Guide RNA Designer — Find Cas9 / Cas12a Targets
Scan a sequence for SpCas9, SaCas9 or Cas12a guide candidates with PAMs and scoring.
🔒 Local processing — pasted sequences are not uploaded
Find protospacer and PAM candidates in a target DNA sequence. Paste a sequence, choose a nuclease (SpCas9 NGG, SpCas9-NG, SaCas9 NNGRRT or Cas12a TTTV), and the tool lists candidate guides on both strands with position, spacer sequence, PAM and GC content. Warnings for poly-T terminators and homopolymer runs, plus a transparent heuristic score, help you shortlist candidates for downstream off-target checking.
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Paste a target sequence to find guide candidates.
Scope: the score is a transparent rule-of-thumb (GC content, poly-T terminators, homopolymer runs) to help you triage candidates — it is not a validated on-target efficiency prediction like Doench 2016. Off-target risk is not assessed: that requires aligning each guide against your target genome. Always verify shortlisted guides with a genome-aware specificity tool before ordering.
How to use the CRISPR gRNA Designer tool
- 1Paste the target DNA region (raw or FASTA).
- 2Pick the nuclease / PAM and whether to search both strands.
- 3Review the ranked guide candidates, their PAMs, GC and warning flags, then shortlist for off-target checking.
Frequently asked questions
- Which nucleases and PAMs are supported?
- SpCas9 (NGG, 20 nt spacer), SpCas9-NG (NG), SaCas9 (NNGRRT, 21 nt) and Cas12a/Cpf1 (TTTV, 23 nt, 5′ PAM). Both strands are scanned and coordinates are reported on the forward strand.
- What does the score mean?
- It is a transparent rule-of-thumb (0–100) that penalises GC content outside the usable range, poly-T tracts that terminate Pol III transcription, and long homopolymer runs. It is a triage aid, not a validated on-target efficiency model like Doench 2016.
- Does it check off-target sites?
- No. Off-target assessment requires aligning each guide against your target genome, which an in-browser tool can't do. Use this to shortlist candidates, then verify them in a genome-aware specificity tool before ordering.