Bug fix to bounds checking of cons[p]. Remember it's not start..end
but 0..end-start.

Inconsequential update to the scoring functions; the match and
mismatch costs are now #defines (but the same as before).


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden@3651 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1