[BiO BB] Designing degenerate primers

[Nagesh Chakka]

Hi all,
I need to design primers to "fish out" the region of interest from 
reptilian genomic sequence. I donot have the reptilian gDNA sequence 
information to design the primer with exact sequence. Hence I thought of 
designing degenerate primers based on the available sequence information 
(eutherian mammal, marsupial, amphibian). Are there any available 
programs which does this kind of primer design or that I need to perform 
a multiple sequence alignment and look for the most conserved region and 
design primer with that.
Any advice is greatly appreciated.
Thanks
Nagesh