Distributions of C (compactness) values calculated for the actual and reshuffled genomes. In each panel, the x-axis represents the C values of the genome in different conditions (L and S phases); the y-axis is the density. Both the “overall” and “remote” operon/gene pairs in the regulons/biological pathways are illustrated respectively, where “remote” means an operon/gene pair whose sequences are separated by at least 100 operons/genes in between on the genome sequence. The black vertical dash line shows the C value for the actual arrangement (in the 3D genome) of the overall/remote operons in regulons for the L phase (a)/(c) and S phase (b)/(d) or the overall/remote genes in the biological pathways for the L phase (e)/(g) and S phase (f)/(h). The 10 colored curves in each panel show the distributions of the corresponding C values for the randomly reshuffled genomes at different percentages (X% where X = 10, 20… 100, from right to left), respectively. Each colored curve was calculated using 100,000 random permutations of the current arrangement of the considered unit (operon or gene) in the genome.