To limit the number of 'special' character you may have in a matching text, you could use this: 
/[RYMKSWHBVDN]{0,2}/i

[download]
However, I'm not quite sure how to integrate this piece that would also satisfy this requirement: 
any number of A,T,C,G ...
Could you try something along those lines: 
/[ATCG][RYMKSWHBVDN]{0,2}/i

[download]
Oww, but then, they could be mixed right?

UPDATE: Oh well, I believe solution offered by ferrency is somewhat closer to what you need (Note: I didn't notice his solution until I actually submitted my alternative ;/)

_____________________ 
$"=q;grep;;$,=q"grep";for(`find . -name ".saves*~"`){s;$/;;;/(.*-(\d+)
+-.*)$/;$_=&#91"ps -e -o pid | "," $2 | "," -v "," "]`@$_`?{print"
++ $1"}:{print"- $1"}&&`rm $1`;print"\n";}

[download]

In reply to Re: self limiting regex help by vladb
in thread self limiting regex help by spq

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