Query a multiple alignment file

[ksw9]

Hi,
I generated a multiple alignment of 3 bacterial genomes with MUGSY. I am interested in identifying which nucleotide positions in the 3 genomes align with each other. For example, if I am interested in variation at position 30 in reference genome 1, I am interested in what position in reference genomes 2 and 3 this corresponds with. Is there a way to query .maf files like this?

Thank you!

[ksw9]

To clarify my original question--if you generate a multiple alignment with a program such as MUGSY, how can you set a reference genome? I am interested in determining where variants occur with respect to a reference genome, for which I have annotations, so it is important that my alignment is with respect to the reference positions.
Any help would be great! Thank you!

[gsgs]

reference genome could be the one with fewest differences
to the others (in average, or the sum).
Or at each position you could take the nucleotid that occurs most often.

Getting all the nucleotides at each position should be straightforward ?!
But I don't know about MUGSY

in the alignments, there are typically "-" s included.
So original position 30 corresponds to the 30th position in the alignment
that has no "-" for that sequence