A method is provided for predicting an amount of methylation of at least one target region. The method includes establishing an observed size of a plurality of oligonucleotides relative to a size standard and correlating the observed size to a number of each of nucleotide base in each of the plurality of oligonucleotides. A mobility coefficient can be determined for each base of each respective oligonucleotide and the determined mobility coefficients can be applied to a predetermined number of polynucleotides subjected to methylation detection analysis. The plurality of oligonucleotides are treated with a modifying agent to obtain amplicons in methylated and unmethylated target regions and amplicons derived from methylated and unmethylated target regions are distinguished based on their relative mobilities. The degree of methylation can be predicted based on distinguished methylated regions.
