You interpretation is correct. Use /g and Perl will keep track of the position in the string itself: 
$rna =~ s/(...)/$gencode{$1}/g;

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لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

In reply to Re: Keeping track of substituted regions with a while loop by choroba
in thread [SOLVED] Keeping track of substituted regions with a while loop by enderk

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