A system for screening nucleotide sequences, a method therefor, a program, a recording medium, and a server on which the screening of nucleotide sequences is executed. The solution comprises a step of storing target nucleotide sequence data and a probe nucleotide sequence, a step of generating complementary sequence data from a probe nucleotide sequence that may be bound to the target nucleotide sequence, and storing a maximum acceptable edit distance between the target nucleotide sequence and the probe nucleotide sequence, a step of reading out each nucleotide sequence data and the maximum edit distance from each storing unit, and evaluating the binding possibility of the target nucleotide sequence data and the complementary sequence data in descending order of edit distance, and a step of storing the result of the binding evaluation in a storage unit.