Suppose we have a snippet of coding region DNA, encoded as base pair letters "ATCGTTGAAT..."

Interesting and excellent example, a base is a letter,a codon is 3-bases long, but, the snippet above denotes a single base letter and not a paired base letter - where every opposing base is counted as a letter -

# 10 base pairs
ATCGTTGAAT
TAGCAACTTA

# 10 bases
TAGCAACTTA
[download]

how can we rectify that to maintain relevance to Perl and Biology ??