An instrument for detecting and measuring fluorescence, comprising: a reaction region holding assembly comprising wells for holding a plurality of spaced-apart reaction regions; a light emitting source adapted to direct excitation beams toward the plurality of reaction regions and to simultaneously illuminate two or more of the spaced-apart reaction regions, the light emitting source comprising an array of light emitting diode sources that are arranged in groups, wherein different groups of predetermined numbers of light emitting diode sources are configured to emit different excitation frequencies; a collimating lens system disposed along a path of excitation beams between the light emitting source and the plurality of reaction regions, wherein the collimating lens system is capable of transforming excitation beams emitted from the light emitting source into two or more spaced-apart bundles of excitation beams parallel to the optical axis of the collimating lens system, and wherein the instrument is capable of directing each of the two or more bundles of parallel excitation beams toward a respective reaction region of the plurality of reaction regions; a focusing lens (30,35) disposed along a path of at least one of the two or more spaced-apart bundles of parallel excitation beams between the collimating lens system and the plurality of spaced-apart reaction regions; a detector disposed to receive emission beams emitted from each of the plurality of reaction regions; and a transition filter (60, 61, 62) that reflects or passes the two or more spaced-apart bundles of parallel excitation beams and that respectively passes or reflects the emission beams to the detector. a reaction region holding assembly comprising wells for holding a plurality of spaced-apart reaction regions; a light emitting source adapted to direct excitation beams toward the plurality of reaction regions and to simultaneously illuminate two or more of the spaced-apart reaction regions, the light emitting source comprising an array of light emitting diode sources that are arranged in groups, wherein different groups of predetermined numbers of light emitting diode sources are configured to emit different excitation frequencies; a collimating lens system disposed along a path of excitation beams between the light emitting source and the plurality of reaction regions, wherein the collimating lens system is capable of transforming excitation beams emitted from the light emitting source into two or more spaced-apart bundles of excitation beams parallel to the optical axis of the collimating lens system, and wherein the instrument is capable of directing each of the two or more bundles of parallel excitation beams toward a respective reaction region of the plurality of reaction regions; a focusing lens (30,35) disposed along a path of at least one of the two or more spaced-apart bundles of parallel excitation beams between the collimating lens system and the plurality of spaced-apart reaction regions; a detector disposed to receive emission beams emitted from each of the plurality of reaction regions; and a transition filter (60, 61, 62) that reflects or passes the two or more spaced-apart bundles of parallel excitation beams and that respectively passes or reflects the emission beams to the detector.