The quality of sequence is dependent on the quality of the template DNA and the respective primers. DNA and primers should be free of proteins, salts, and organics. PCR template should be free of extra primers and dNTPs. For the highest quality plasmid DNA, we recommend using  Qiagen QiaPrep Spin, Eppendorf Fast Plasmid Kit, or Millipore Montage 96-well plasmid prep.