CRISPR Adaptation: Spacer Acquisition Simulator

Most CRISPR demos jump straight to Cas9 cutting DNA. This one models the step that has to happen first: bacterial adaptation, where a Cas1–Cas2 integrase complex samples fragments of invading phage DNA, preferentially selects the ones flanked by a correct PAM sequence, and splices them into the bacterium's CRISPR array as new spacers — almost always at the leader end, so the array grows into an ordered timeline of past infections. Tune PAM stringency and leader-end integration bias to see how selective vs. sloppy immune-memory formation looks, and watch live fidelity and rejection counters track how "clean" the resulting array is.