ad 0
Without programming (e.g., on a piece of paper), find the optimal local alignment of sequences 
CCCGTGTAA and GTATA, with the following parameters: 
gap penalty -1, mismatch -2, match 1. What is the score of this alignment?

# GTA
# GTA

# - or -

# GTA-A
# GTATA



ad 1

basic usage where we set the properties looks like:
Align.PairwiseAligner(match_score=1, mismatch_score=-2, gap_score=-1, mode='local')

and then after alignment of "CCCGTGTAA" & "GTATA" we get:
target            5 GTA 8
                  0 ||| 3
query             0 GTA 3


ad 2
histones_dict = SeqIO.to_dict(SeqIO.parse("histones.fa", "fasta"))