Guide-RNA Off-Target Risk Scanner

Guide RNA design

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Scan speed 40 nt/s

Live scan readout

Genome scanned

On-target site

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High-risk sites

Moderate-risk sites

Off-target risk score

Poor vs. screened

Guide	Sites	Score
Poorly-designed	–	–
Well-screened	–	–

How it works

Before a guide RNA is ever used to cut DNA in a real cell, bioinformatics pipelines align its sequence against the entire genome, sliding a 20-nucleotide window across every position and counting mismatches. A window with very few mismatches is a plausible off-target cutting site, because the CRISPR–Cas9 complex tolerates some sequence slack.

This scanner does exactly that: it slides the selected guide across a synthetic genome and colors every scanned position by mismatch count — green (safe, many mismatches), yellow (moderate similarity), red (near-perfect off-target match), or the single blue on-target hit.

Poorly-designed guide — chosen without a genome-wide check; several near-identical sequences happen to exist elsewhere, each a real off-target risk.
Well-screened guide — deliberately selected because the genome-wide search found no other close matches; only the intended on-target site lights up.
Risk score — a weighted count of flagged sites (high-risk sites weigh more than moderate ones), a rough proxy for the metrics real design tools like CFD/MIT scores report.

On-target High-risk off-target Moderate risk Safe / no match