To enable accurate analysis of a base sequence even in an electrophoretic pattern containing a degraded part. The base sequence of a nucleic acid is determined by conducting the following steps (A) to (C) in this order: (A) a basic peak extracting step wherein basic peaks are extracted from electrophoretic data involving the respective peaks of the four bases obtained by electrophoresing a sample nucleic acid; (B) a condition determining step wherein a basic peak at the search starting point, from which the search is started, and a standard peak-to-peak distance are determined based on the time-series data composed of the basic peaks extracted above; and (C) a base sequence determining step wherein peak-to-peak intervals are successively scanned forward and backward in the above-described time-series data starting from the basic peak at the search starting point and then the peak-to-peak distance is compared with the standard peak-to-peak distance as determined above so as to add an interpolation peak to a peak-missing area.