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(A) Enumerating all possible coding sequences for small tag proteins reveals that the coding sequence with the lowest energy for its MFE structure (blue star) is not always the same as the coding sequence with the lowest AUP (red star). (B) MFE structures for mRNA solutions for the HA tag that minimize AUP, minimize free energy, and maximize codon adaptation index (CAI), with nucleotides colored by their computed probability of being unpaired.
