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Although we have established the amino acid sequence necessary for the primer, this is not the only required step. Next, the specific base pair sequence must be found. The sequence of codons to be used is essential. Two concerns must be met:
 * For the unaltered parts of the primer, the codons must be the exact same ones as in the original section of the sequence. This is essential, as all other variables must be kept constant for the test to be valid.
 * The altered segment of the primer must have a codon with similar frequency as the original amino acid codon. Frequency in this case simply refers to out of the number of times the amino acid appears, it is this specific codon. maintaining a similar frequency is important because while the end result (namely, the amino acid) to be coded for is the same, other variables, such as folding time in the secondary structure, may differ between codons. Maintaining a similar frequency gives us the best odds of matching these other variables.