CRISPR-Cas9 Target Search & Cleavage Simulator

Genome editing with CRISPR-Cas9 works because the Cas9-sgRNA complex is a molecular pattern-matcher: it slides along double-stranded DNA, pauses only at short PAM motifs, and tests base-pairing with its 20-nucleotide guide RNA outward from the PAM as an expanding R-loop. This simulator renders a real 3D DNA double helix, seeds it with one true on-target site and several PAM-bearing decoys carrying random seed and distal mismatches, and lets Cas9 search, test and either reject or cleave each one according to the same PAM-proximal seed sensitivity seen in real biochemistry. Raise the nuclease fidelity to watch off-target cleavage collapse toward zero while the perfect match still gets cut every time — the exact trade-off engineered Cas9 variants are built to solve.