The present invention relates generally is a method for determining the likelihood that a test polynucleotide sequence differs from a driver polynucleotide sequence. More particularly, the present method uses fluorescence-based technology in the assessment of the results of competitive hybridization between polynucleotide sequences. The present method does not require nucleotide sequencing or gel electrophoresis and is capable of being multiplexed and automated. The methods of the present invention will find broad application in the analysis of polynucleotides, inter alia in genetic analysis, specific locus testing, genotyping, mutation detection, the discovery and detection of single nucleotide polymorphisms (SNPs) and mapping.