my @gene = split //, $seq[$i];
my $count = @gene;
if($i < $#seq) { 
    push @gene, split //, substr $seq[$i+1], 0, 3;
}
# Now, proceed as before:
for (my $i=0; $i<$count; $i+=3)    {
    ...
}

##</code><code>##

   substr($genestring, $i, 1)