One more clarification. In assignment 2A, I want you to look at the SP score with affine gap costs by taking the multialignment and then extracting all pairwise alignments. Then you strip away all indel-only columns before you compute its score. This means that
AAACCC---AAA AAA------AAA
should be changed to
AAACCCAAA AAA---AAA
and then have the score computed.
Hope this helps!