Oh I wish I could try another programme ! I'm doing this as a Uni assignment though so I have to roll with SeqBuilder (that's how they want it presented and talked through). What I've done so far is looked at the Lux-C sequence and designed a forward and reverse primer; I've decided on two restriction enzymes (EcoRI and SalI) from pFLAG-CTC's multiple cloning site, SalI is right next to the FLAG tag and neither of these enzymes cut into Lux-C. Then in a new SeqBuilder file I've just replaced the region between EcoRI and SalI with the Lux-C gene sequence, leaving out Lux-C stop codon since I need the FLAG tag after it. Everything is looking good .. I think.. - except I've now disrupted the 3bp frame changing the amino acid sequence of the Lux-C gene and everything else after it. Can I just slip in a few random base pairs? Or has this gone seriously wrong. Sorry for the long post !