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But, of course, if you change:
bases=`echo A T G C`to:
bases=$(echo A T G C)
your script should work just fine with bash, ksh, or zsh. And, if you use the much simpler and more efficient:...

bash -c 'b="A T G C"; for c1 in $b;do for c2 in $b;do for c3 in $b; do echo $c1$c2$c3;done;done;done'Hope this works/helps...

Update: The commands don't need to be squashed in one line though...

awk '$2 != $3 {print}' file