As the title says, I'd like to know if there's a set convention for matching dna/rna/aa letter symbols (that is ACGT for DNA, ACGU for RNA, and a lot more letters for AAs) with some properly defined colors (for example, DNA letters might be <span style="background-color:Green">A</span>: green, <span style="background-color:Blue">C</span>: blue, <span style="background-color:Yellow">G</span>: yellow/black and <span style="background-color:Red">T</span>: red)? The idea is that such colors would then be used in the areas for better recognition of the characters. Thanks!
As far as I know, there are no standards for colors. Each program uses slightly different colors.

You might consider using the same colors as JalView: http://www.jalview.org/help/html/colourSchemes/

Here are the available options for nucleotides in Geneious:

<img alt="" src="http://i.imgur.com/kuYCD2l.png" />

And here are the available options for amino acids in Geneious:

<img alt="" src="http://i.imgur.com/zhxauCR.png" />