Provided are: a method for designing primers to be subjected to a polymerase chain reaction, the method including a local alignment step for determining the local alignment score of primer candidate base sequences by conducting pairwise local alignment under the condition that the partial sequences compared include the 3' end of the base sequence of the primer candidates, and a global alignment step for determining the global alignment score by conducting pairwise global alignment of base sequences of a preset sequence length including the 3' end of the base sequence of the primer candidates; and a primer set.
