We present a segmentation algorithm capable of segmenting exercise repetitions in real time. This approach uses subsequence dynamic time warping and requires only a single exemplar repetition of an exercise to correctly segment repetitions from other subjects, including those with limited mobility. This approach is invariant to low range of motion, instability in movements, and sensor noise while remaining selective to different exercises. This algorithm enables responsive feedback for technology-assisted physical rehabilitation systems. We evaluated the algorithm against a publicly available dataset (CMU) and against a healthy population and stroke patient population performing rehabilitation exercises captured on a consumer-level depth sensor. We show that the algorithm can consistently achieve correct segmentation in real time.