## Additional file 8.
bcd mRNA sphere was systematically moved either along the A-P axis (panels A-C; Rx denotes distance from anterior pole) or along the D-V axis (panels D-F; Ry denotes distance from the A-P axis). We also systematically changed the ratio of B_{bound}/B_{free }at nuclear cycle 10 (panels G-I). Here, the shape of the simulated embryo is the same
as in Fig. 5; for reference, the parameter values used in the simulations shown in Fig. 5 and Fig. S6 are marked with arrowheads. The resulting Bcd gradient profiles on the
dorsal and ventral sides were then evaluated for their B_{max }values (A, D and G), λ values expressed as either c or x (B, E and H), and the values of Δx_{Bcd }and Δc_{Bcd }at target boundary positions of both Hb and Otd (C, F and I). As shown in individual
panels, these simulated results remain consistent with the three experimentally observed
properties: 1) B_{max }is higher on the dorsal side than on the ventral side (A, D and G), 2) λ measured as either x or c is larger on the ventral side than on the dorsal side (B, E and H; compare dashed
lines with solid lines), and 3) Δx_{Bcd }at target boundary locations is larger than their corresponding Δc_{Bcd }(C, F and I; compare blue lines with red lines). As further discussed in the theoretical
consideration above, the value of Δx_{Bcd }- Δc_{Bcd }in the middle section of the embryo reflects the geometric properties of the embryo.
This value is 11.1 μm at x_{Hb}/L in our simulation results shown in this figure and, as expected, is insensitive to
bcd mRNA location or the B_{bound}/B_{free }ratio. It is also fully consistent with both experimental (10.7 μm as shown in Fig. 4A) and theoretical values (11.7 μm as shown in Fig. 1C).
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