Degenerate primers for direct fragment sequencing

[amerotto]

I am sequencing fragments from Cyperus difformis (Plant, cyperaceae). I
am using
degenarate primers in order to isolate the fragments that I want. For
some
primers/template combination I had good results, but for another the
sequence just not
appear or appear with double peaks. I am using the Qiagen gel cleaning
kit and the
Sigma spin column for the cleaning procedures.

Question: Are degenerate primers a problem for sequencing? If yes, how
can I compensate
for that?

Thanks

Aldo


Aldo Merotto