Methods are described for analyzing at least one polymorphic site in a biological sample containing at least one single-stranded template, including the steps of: combining the biological sample with a primer specific for each polymorphic site in each template and a primer extension preparation, to form an assay mixture; wherein the preparation includes: chain terminating nucleotides forming a first nucleotide class, chain elongating nucleotides forming a second nucleotide class such that the second nucleotide class does not include a nitrogenous base present in the first nucleotide class, and a template-dependent nucleic acid polymerase; incubating the mixture for a time and at a temperature sufficient to extend each primer by addition of at least one nucleotide; and determining the size of each extended primer. Kits suitable for practising the invention are also provided.
