SnapGene uses the BLOMSUM62 scoring matrix (see https://en.wikipedia.org/wiki/BLOSUM) with a threshold of 1, in order to classify aligned residue pairs as Identical, Similar or "Not Similar".
For example, the Threonine/Isoleucine (T/I) pair at position 22 in the alignment below has a BLOMSUM62 score of -1, which is below the threshold of 1, so the pair is marked "Not Similar".
