Shaded Annotated Sequences:
GeneWorks and DNAStar will accomplish this. If you'd like to save
yourself a few thousand francs, 13 point Courier and most any
reasonably well constructed drawing program will suffice.
As for fonts, Courier is the only postscript font I have seen
that is truly monospaced. There are several bitmapped-only
fonts that are monospaced, but they all share the trait of
getting mangled during manipulation and printing.
Standard Weasel Clause:
I have no affiliation with Adobe Systems, Apple Computer, DNAStar,
Intelligenetics, or the International Brotherhood of Electrical
Workers. The University of Illinois does not even know I exist, much
less condone my opinions.