A system for conducting a capillary electrophoresis assay includes a light source, an interface, and an illumination optical system. The light source is configured to provide a source beam of electromagnetic radiation. The interface is configured to receive a plurality of capillaries containing one or more target molecules or sequence of molecules. The illumination optical system is configured in use to produce a plurality of output beams from the source beam and to direct each of the output beams to corresponding capillary of the plurality of capillaries.