A real-time, automated, nucleic acid sequencing apparatus that offers high speed, definitive sequencing on many samples at the same time. The apparatus permits more than one clone to be sequenced at a time, thus vastly decreasing the time required to sequence longer fragments and reducing sequencing costs accordingly. The apparatus detects electromagnetic radiation from a plurality of lanes in an electrophoresis system wherein the plurality of lanes are arranged in a planar array. The apparatus includes an optical system for detecting the radiation at a plurality of wavelengths and is made up of a collection element, a filter for selectively transmitting the plurality of wavelengths received from the collection element, and a detection system for measuring intensity of the radiation received from the filter means. A translational stage is used for mounting the optical system and for moving the optical system parallel to the planar array in order to move the collection element back and forth across the lanes in order to receive radiation from the lanes, one lane at a time during electrophoresis. Also included is a computer system for controlling the filter and the stage, and for receiving intensity data from the detector and correlating that data with the corresponding lane and corresponding wavelengths transmitted by the filter in substantially real time.