The solution has two phases: initialization and steady state.
During initialization the three complement elements of each element on the match pattern are computed. They are then distributed to the register wheels. This takes about 100 cycles, because almost the entire layout was designed with only the steady state in mind.
During the steady state individual elements from the sample are compared with elements from the pattern. This happens 12 times per sample. The precomputed complements allow each comparison to happen using just one unification attempt. The result of a comparison is a water that might appear next to the piston at the top. The top left mechanism then decodes the actual output from those waters.

Fun facts:
1. Critelli does not get used.
2. Things sometimes get crowded around arm 32 (the Z-Track in the middle), but nothing collides. In fact that track could support another arm during the steady state.
3. The input not-gate returns, this time with gold.
4. The salt input doubles as disposal, should a comparison fail.