Studying the structure and variation of repetitive DNA sequences remains an unsolved problem. In a collaborative paper between our lab and the Emerson lab at UC Irvine, we assembled highly repetitive pericentromeric regions of Drosophila melanogaster using highly accurate (HiFi) long reads. We provided a new framework to study genetic variation in such repetitive regions. Our study offers new insights into the evolutionary and molecular mechanisms underlying the patterns of genetic variation in two such clusters: the Histone and Stellate gene clusters.