In this study we introduce distinct fluorescent tags flanking a range of genomic regions and track the motion of the labelled reporters using an OMX Blaze microscope. We describe a work flow that enables 3D live cell tracking with a mean measurement error of 63 nm. We find that within individual yeast cells the separation of operator sequences exhibits substantial variation over time. Genomic loci are able to reorganize extensively below a threshold of approximately 70 kb. However above this, there is a transition to independent motion constrained by the nuclear environment. Within a clonal population of cells the mean conformations of reporter loci vary significantly and can persist over time frames of 1-10 minutes. By comparing chromatin states in related mother-daughter cell pairs we observe no evidence for inheritance of chromatin conformation.