Using your own multiple sequence alignment:

If you already have a multiple sequence alignment containing the sequence you wish to clone as well as the associated homologues, you can skip the BLAST and sequence extraction stages.

Note that if this is the case, AutoCloner expects the multiple alignment to 1) be in Fasta format with gaps indicated by “-“ and 2) for the sequences to be in the following order: sequence to be cloned, same sequence but with flanking regions included, then any homologues.