pick sequencing primers to cover a whole sequence

[Fernan Aguero]

Is there an app within emboss that would allow me to pick
sequencing primers to cover a whole sequence?

Say I have a sequence of 3-5 Kb that I want to sequence
completely. I want to place primers each one separated
around 400 bp on each strand. I can do this manually, but
what if I have a reasonable number of this kind of
sequences? I'd like to use a primer design program to
discard primers with loops, hairpins, poor 3' ends, etc. and
also to produce primers compatible with automated sequencing
conditions.

Perhaps someone can point me to an external program, if
emboss currently doesn't carry any with this functionality.

Or perhaps I can fool primer3 by tweaking some parameters? 

Thanks in advance,

Fernan

-- 
F e r n a n   A g u e r o
http://genoma.unsam.edu.ar/~fernan