= Template-dependent mismatch weights
A mismatch's <Boltzmann weight> relative to the correct pair depends on which base is the fixed template, not just on the unordered mismatch name. In a rigid two-versus-three-hydrogen-bond cartoon, replacing the incoming base with the same wrong pair can lose a different number of bonds for the opposite template orientation. Proofreading and nonequilibrium polymerase discrimination make such pair-energy weights insufficient as a complete replication-error model.
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