Parameter sensative alignment scores

[alancleary]

As @adf-ncgr pointed out in issue #161, the score and threshold alignment parameters need to be adjusted relative to the size of the query/result tracks. For users not familiar with the nuances of the various parameters, the adjustment or even the need for it may not be apparent. The parameter should be revised such that the quality of the alignments is invariant relative to the size of the query/result tracks. Not sure how exactly this should be done - perhaps by moving to a percent matched/mismatched/indels tolerated approach?