Fig. 1.

Toy example of a spaced-word match (SpaM) between two DNA sequences S₁ and S₂ with respect to a binary pattern P = 1101001, representing match positions (‘1’) and don’t care positions (‘0’). The same spaced word AT*G**C occurs in both sequences. A SpaM corresponds to a local gap-free pairwise alignment with matching nucleotides at all match positions of P, while mismatches are allowed at the don’t care positions. Note that, in practice, we are using much larger patterns than in this example; by default, App-SpaM uses a single pattern with 12 match positions and 32 don’t care positions.