A system for performing capillary electrophoresis of multiple samples comprises a capillary containing a separation medium and having inlet and distal ends and an interrogation region; a power source configured to apply voltages between inlet and distal ends; and logic to cause execution of: applying a first substantially constant forward polarity electrophoresis voltage to the capillary; before all of the first DNA fragments have passed the interrogation region, applying a reverse polarity voltage pulse to the capillary, thereby transporting at least some of the first DNA fragments in the capillary toward the capillary inlet; introducing a second sample to the capillary inlet, the second sample comprising second DNA fragments having a plurality of different sizes; and applying a second substantially constant forward polarity electrophoresis voltage to the capillary to simultaneously perform electrophoresis on the second DNA fragments and the first DNA fragments.