Table 1. List of main symbols used in this paper.

	Total Bcd concentration
	Total concentration of binding sites
	Concentration of unbound binding sites
	Concentration of site-bound Bcd (or of Bcd-bound sites)
	Concentration of free Bcd
	Concentration of site-bound fluorescent Bcd
	Concentration of free fluorescent Bcd
	Concentration of site-bound non-fluorescent Bcd
	Concentration of free non-fluorescent Bcd
	Dissociation constant, , of scheme (5)
	Diffusion coefficient of free Bcd
	Diffusion coefficient of free and Bcd-bound sites
	Collective effective diffusion coefficient (Eq. (2))
	Single molecule effective diffusion coefficient (Eq. (2))

The concentrations listed above satisfy the following relationships: , , , . In equilibrium they also satisfy other relationships (see supplementary text 0.2). Since we work with data obtained under different conditions in parts of the text we also use the following superscripts: to identify values derived from FCS experiments performed in the cytoplasm during interphase (i.e. cytoplasmic values during interphase at a position along the embryo that corresponds to the one probed with FCS experiments); to identify values derived from FRAP experiments performed in the cytoplasm during mitosis (i.e. cytoplasmic values during mitosis at a position along the embryo that corresponds to the one probed with FRAP which we assume is the same as the one probed with FCS) and to identify values derived from FCS experiments performed in nuclei (again at the location along the embryo that is probed with FCS).