Table S1.

Domain statistics and simulation of expected domain size and gene number

Stage	Domains (n)	Genes (n)	Median domain length (bp)	Expected median domain length (bp)	Median genes per domain	Expected median genes per domain	Mean domain length	Expected mean domain length	Mean genes per domain	Expected mean genes per domain
EE active	1,046	6,047	13,054	4,506	4	1	25,318	9,492	5.8	2.0
EE border	2,013	1,914	2,461	600	1	0	5,272	1,865	1.0	0.4
EE regulated	1,041	9,424	23,874	13,647	4	2	42,358	21,696	9.1	4.6
L3 active	1,274	6,198	13,608	4,328	3	1	22,184	8,587	4.9	1.8
L3 border	2,471	1,996	2,405	500	1	0	4,343	1,794	0.8	0.4
L3 regulated	1,257	9,220	18,670	11,567	3	2	33,619	18,503	7.3	3.8