added new attributes to Alignment object

this provides the necessary framework for the skbio aligners to return the same object for a consistent interface.
Maybe change the first sentence to be "The start/end positions indicate the range of the unaligned sequences in the alignment".

And break up "For example, if local alignment was performed on the sequences ACA and TACAT, depending on the specific algorithm that was used to perform the alignment the start/end positions would likely be: [(0,2), (1,3)], indicating that alignment looked like the following, and that the first and last positions of the second sequence were not included in the alignment" 
Into: "For example, if local alignment was `should this be a 'were'?` performed on the sequences ACA and TACAT, depending on the specific algorithm that was used to perform the alignment the start/end positions would likely be: [(0,2), (1,3)]. Indicating that the first and last positions of the second sequence were not included in the alignment. The result would look like this:"