The hydro letters are too dark to be visible on the dark background: the AAs are less visible than gaps, which is bad. A picture is worth a thousand words, I was told:

(An a3m is not quite a fasta, but it highlights fine.)

I'm not familiar enough with hydrophobicity scales to immediately tell which of the ~dozen scales of this kind the color scheme is based on, but uh. I suggest doing the following:

• Make gaps a less obvious shade of grey, maybe grey70.
• Use a new color scale to map the numbers to colors. RdYlBu from colorbrewer is roughly in the same neighborhood of this one.

I think I can make a proof-of-concept with that old '82 hydropathy scale (which stretches nicely from -4.5 to 4.5) later. Like, in 48 hours.