The present invention provides methods and kits for identifying nucleotides at a variant site in a target molecule by forming fluorescence resonance energy transfer labeled product. The location and type of fluorescent labels in the labeled product provide strong signals and relatively high spectral purity that facilitate detection. Utilizing various secondary labels and different combinations of acceptor and donor labels, certain methods permit multiple analyses to be conducted simultaneously and at high throughput. The methods can be used in a variety of applications such as analyzing point mutations and single nucleotide polymorphisms (SNPs). In addition, the methods have utility in other applications in which specific sequence information is of value, including detection of pathogens, paternity disputes, prenatal testing and forensic analysis.