Mammalian system have a large genome with a high level of gene sequence identity from other genomic DNA, making assessment difficult and time-consuming.Our findings describe a simple method for rapidly isolating and amplifying HoxA loci in the mouse genome using degenerate primers. For the semi degenerate primers,they were designed based on cognate gene coding regions of consensus sequences. After assembling sequences from different primer matches amplifying the same HoxA loci, the effects of the universal primer-template match on the efficiency of standard PCR amplification were investigated. Touchdown PCR increased specificity and yield in two consecutive amplifications on different gel concentrations by using high and low annealing temperatures. This method was quick, simple, and inexpensive for amplification of consensus sequences in very large gene sequences.