While homeoboxes are the same, they are landing places for homeotic genes. They don't themselves direct which genes are turned on or off or, thus, what organisms look like.
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Homeoboxes are landing pads for helicopters-- any helicopter can land there, anything from a cheap $10/ride copter from the county fair to an advanced Apache attack helicopter. The different proteins which use homeoboxes to land are like these different kinds of helicopters, which obviously can do very different things.