ENH: added score and start_end_positions

fixes #471, this allows the Alignment object to be returned as a result from
the various aligner functions.
MAINT: made score/start_end_positions attributes of Alignment rather than SequenceCollection, since they are only relevant in the latter case
MAINT: fixed error in doc, thanks @ebolyen
MAINT: improved doc string wording, thanks @ebolyen
Merge pull request #472 from gregcaporaso/issue-471

added new attributes to Alignment object