In a method of identifying an unknown nucleotide sequence using base addition, a sequence of bases is obtained from a template, a base in the sequence is identified as an unknown base, an "unknown" indicator is included in the sequence, and an output sequence is generated containing the unknown base indicator. The sequence of bases is obtained from the template by evaluation of a reporter and assigning the bases in accordance therewith. A determination is made as to whether the reporter is from a preceding cycle of base determination, and if the reporter is from a preceding cycle of base determination, the base assignation is discarded.