Blurry sequencing

[Thomas E Darga]

Can anyone help me alleviate a blurry sequence problem with cDNA sequencing?

I'm sequencing a randomly and oligo dt primed directional cDNA library and am
having problems with the 3' end of the poly A containing clones. Also having
problems with the clones containing poly nt stretches. The problem is that
the sequence is clean from either end until I reach the poly nt stretch, when
all lanes have bands of different intensities as if there are multiple cDNA
species of a few bp difference in length. The mfgrs recommended reducing the
extension temp of the PCR and Seq rxns, but it hasn't seemed to alleviate
the problem.

Thanks