[AndrewOMartin]

The compression ratio will likely skyrocket if you sorted the list of bases.

[shellfishgene]

You're joking, but a few bioinformatics tools use the Burrows-Wheeler transform to save memory, which is a bit like sorting the bases.

[jefftk]

You can also improve compression by reordering the sequences within the FASTA file, as long as you're using it as a dictionary and not a list of title-sequence pairs.