Abstract Accurate repair of DNA double-strand breaks (DSBs) is essential for genome stability, and defective repair underlies diseases such as cancer. Homologous recombination uses an intact homologous sequence to faithfully restore damaged DNA, yet how broken DNA ends find homologous sites in a genome containing billions of non-homologous bases remains unclear. Here, we introduce sister-pore-C, a high-resolution method for mapping intra- and trans-molecular interactions in replicated chromosomes.