Download mds42 gbk with actual sequences (previously had no sequences in the file).
Modified the GraphSearchCodonReplacer algorithm to use error scores.

So, now for every possible codon extension the algorithm checks that the
result is not too far from the pre-computed feature profiles of the
original algorithm. For now the two profiles have are GC content
and secondary structure.

One thing that we aren't yet handling is the possible case where we hit
a dead-end because our error-tolerances were too strict. We need to
think about how to deal with this.
Remove unused (and unintelligible) code from refactor.py for building the aa_to_codon dict.
Save the updated caches after using the correct genbank file with sequences.