CRISPR-Cas9 Target Search (2D)

The 3D version of this simulation walks you through CRISPR-Cas9 editing as seven fixed steps you click through by hand. This 2D companion turns the same mechanism into a continuously running search: Cas9 sweeps a 100-nucleotide DNA window end to end at a speed you control, pausing at every candidate PAM site it passes — most of which are decoys it rejects within a fraction of a second — and only fully unwinds the helix at the one true target, where it reads all 20 spacer positions against the guide RNA you designed. Set how many mismatches that guide RNA carries and, more importantly, where — the same mismatch count produces a dramatically different cleavage probability depending on whether the errors sit in the PAM-proximal seed region or the tolerant PAM-distal end, because the underlying weighting mirrors real Cas9 biochemistry. Every completed interrogation ends with a weighted random roll against the live efficiency number, so over many automatic cycles you can watch the success-rate readout converge toward the theoretical value instead of just reading it off a formula.