@ebolyen, we need to add an example of how to go from values of ``cigar``, ``query_sequence`` and ``target_sequence`` to a pair of aligned sequences and/or an ``Alignment`` object. This will be one of the main questions our users have. Also, would be good to *additionally* show ``striped_smith_waterman_alignment`` here as that saves users a few lines of code. 

We should also add an example of aligning multiple targets (from a ``SequenceCollection``) against a single query and show how to find the best match based on ``optimal_alignment_score``. This effectively illustrates non-heuristic database searching. It should be easy to add, so I suggest we do that for this PR.