Combine forward and reverse sequence - (Sep/07/2007 )

Hi there
I have a question concerning the analysis of sequencing results. With very long inserts I usually sequence my clone from both directions, getting a forward and a reverse sequence. I do an alignment on muscle and get the overlapping sequence in the middle (end of forward, beginning of reverse sequence), then I can edit these middle part and want to combine the two parts (delete on of the double stretches) to get one continous sequence of my clone.
How is this best to achieve ? I tried with Genedoc, but somehow I cannot cope with this programm (I do not manage to delete one of the sequence in the double stretches.
I hope I described everything somehow comprehensive, I assume this is rather a standard procedure many people apply.
Please let me know how to do this easiest ?
pET

take the reverse complement of one of the sequences and then take the consensus sequence after stacking them.