Is there a typical use "replace...with..." here?

So "replacing all 321 instances of a specific "genetic three-letter word," called a codon, throughout the organism's entire genome with a word of supposedly identical meaning" means "throughout the organism's entire genome, there are all 321 codons (one codon is a specific genetic three-letter word), and scientists replaced all the codons with 321 instances of a word (all instances of the word have the same meaning, supposedly)"?

Context:

In one project, researchers created a novel genome -- the first-ever entirely genomically recoded organism -- by replacing all 321 instances of a specific "genetic three-letter word," called a codon, throughout the organism's entire genome with a word of supposedly identical meaning. The researchers then reintroduced a reprogramed version of the original word (with a new meaning, a new amino acid) into the bacteria, expanding the bacterium's vocabulary and allowing it to produce proteins that do not normally occur in nature.

More:
http://www.sciencedaily.com/releases/2013/10/131017144628.htm