Figure 1

Example alignment pair. Numbers identify the residues in the sequences. k₁ columns – A5B-, A6B-, A7B5, and A8B6 – are found in only the left alignment. K₂ columns – A7B-, A8B-, A5B5, and A6B6 – are found in only the right alignment. K₃ columns – A1B1, A2B2, A3B3, and A4B4 – are found in both alignments. Alignment identity is I = (2K₃)/(2K₃ + K₁ + K₂) = (2 × 4)/(2 × 4 + 4 + 4) = 1/2.