Abstract: The present invention relates to a method for distinguishing a first nucleic acid sequence from a second nucleic acid sequence by electrophoresis. The first nucleic acid comprises a first common sequence tract, a variable sequence tract and a second common sequence tract and the second nucleic acid comprises a first common sequence tract, optionally an variable sequence tract and a second common sequence tract. The first and the second nucleic acid sequence is contacted with a probe sequence that is reverse complementary to the first and second common sequence tract under conditions allowing the hybridization of the probe sequence to the first and second nucleic acid sequence, thereby forming a first probe hybrid and a second probe hybrid. Subsequently, the first and second probe hybrids are submitted to electrophoresis to detect the electrophoretic mobility of the first and second probe hybrid.