The presented paper deals with a novel algorithm for local pairwise alignment of DNA sequences. It is designed to align nucleotide sequences of various length, to determine the matches of the nucleotides and the matches on the base of the complementary rule indicating them graphically in the alignment result. The performed experiments show the ability of the algorithm to retrieve significant biological information through the alignment. This allows the analysis of biological relationships, evolutional mutations and process. To analyze the performance of the proposed algorithm a comparative analysis with Smith-Waterman algorithm is accomplished. The experimental results show the advantages and effectiveness of the proposed algorithm.