changed output directory for new sequences

Previously, all sequences from the same gene were appended to one file.
This is a misguided approach, because if the script gets rerun after something changes,
I will end up with two sequences from the same species in each file.
Now, separate files are made for each species and they are overwritten if the script is rerun
added code to rename the sequences from augustus so they include the species name
added renaming of Exonerate sequences also
added code to make alignments of all sequences and to concatinate alignments