High Background Level in PCR Product Sequence

Possible Causes:

1) Residual Primers: If residual primers from the PCR reaction are not removed, or if the primer concentration submitted is in excess of the requested amount, the result appears as if there are multiple overlapping sequences. Solutions: Check the concentration of the submitted primer to make sure it is accurate. Purify the PCR product with either Sephadex chromatography or a Qiagen QiaQuick column to remove the residual primers.
2) Multiple Bands: Two or more templates are present in the sequencing reaction resulting in overlapping sequence. Solutions: Run your DNA on an agarose gel to be sure that only one band is present and re-purity if necessary.