Replace leading and trailing lowercase bases in velvet contigs.

Some velvet contigs have lowercase leading and trailing bases.  These
bases generally suggest low coverage in the sequenced region (see
http://listserver.ebi.ac.uk/pipermail/velvet-users/2012-March/001690.html).
We now remove these leading/trailing bases as visual examination of
several alignment types indicates that these bases are incorrect and/or
causing improper alignments.