Which regions of a cDNA fragment is suitable for oligo design?

[Rimantas Kodzius]

Hallo!

Can somebody help me?

I have many cDNA's from A.fumigatus and I want to choose a specific
oligo for every cDNA for hybridization.

I should avoid  DNA sequence from conserved domains.

Do You know some programs, which would be suitable for this purpose?

Thank You very much!

Rimantas.Kodzius at sbg.ac.at