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!