These are the steps I would take:
1) align the sequences
2) read each column of the alignment and produce a list of the different possible amino acids in each position
3) each position can now be represented by a list which is easily converted to a regular expression
For 1st three positions it would be:
Oh, and for crying out loud, if you want to be a biostats grad student, learn some biology!
solved How to write regular expression for given sequence