= Solution
A diagonal <substitution matrix> score measures enrichment over a background match, rather than simply rewarding an identical letter. <tryptophan residues> are comparatively rare, so a W–W match has a small chance background frequency $p_W^2$. Its observed conservation produces a much larger ratio $q_{WW}/p_W^2$ than the corresponding ratio for the more common <leucine>. The <BLOSUM62> diagonal therefore awards W–W more than L–L. Both the background frequency and the observed pair frequency matter; rarity alone does not determine a diagonal score.<Amino acid substitution matrices from protein blocks by Steven Henikoff and Jorja G. Henikoff>[Methods, p. 10916, observed/expected pair ratios; BLOSUM62 score matrix, W–W and L–L entries]{ref}
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