Hi-C contact matrices from 2-4 h (stage 5), 6-8 h (stage 10/11), and 16-18 h (stage 16/17) wild-type embryos, showing constitutive loops between paralogous genes, salr-salm (left), scyl-chrb (middle), and tsh-tio (right). Contact matrices were downsampled to contain the same number of informative reads per time point (377 million useable reads). Note that the LAs at scyl-chrb and tsh-tio interact with a respective third LA (middle LA) forming two smaller loops.
