Do you mean the current index of @DNA when looping?

TIMTOWTDI!

The traditional way with your code is to use an explicit counter:

my $idx=-1;
for my $nucleotide (@DNA){
    $idx++;
    ...
}
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But you can also apply while / each on arrays

while ( my ($idx, $nucleotide) = each @DNA){
    ...
}
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(I tapped this message into a mobile, no guaranty for the code.)

HTH! :)