This study seeks to develop a new tool for sequence alignment search using a possible relationship between hybridization energy values, BLASTN scores, and the BLAST alignment lengths. Additionally, this research explores the validity of alternate alignments by introducing shifts in the original alignments. Directly translated DNA sequences from 96 proteins and 11 non-coding RNA are used to perform a BLASTN search in GenBank. Six shifts, three in the forward direction and three in the backward direction, are introduced to the resulting 29,954 alignments and hybridization energy values are computed for each of the shifted and original alignments. Results indicate a statistically significant linear correlation (R = ±0.967) between the BLAST score and the corresponding hybridization energy values for the original alignments. However, the shifted alignments did not exhibit any important correlation for the same parameters.