A system is disclosed for precisely measuring time intervals, used to either characterize or diminish noise components in repetitive waveforms. An interval timer generates a whole number count of cycles in combination with beginning and ending ramps capable of resolving fractions of a cycle, to accurately register the time interval. Selection logic can be implemented to time either single periods or spans of multiple consecutive periods of the waveforms. Multiple time measurements are arranged in sets, each set corresponding to a different span of “N” consecutive periods over a range of values for N. A variance of each set is generated, and an array of variance vs N provides a function having properties of an auto-correlation function. Instrument jitter can be reduced based on measurements of period spans rather than individual periods, and is reduced in proportion to the increasing size of the measured span. These techniques are enhanced by random statistical samples, obtained by a dithering of the measurement rate. This also diminishes the impact of aliasing products.