You don't need to make a bitstring. Replace input, chunks at a time.

my %chunkmap =
    map { $_ => pack "b*", @charmap{split //,$_} }
    map { glob }
    map { ("{A,C,G,T}" x $_) . ("A"x(4-$_)) }
    1..4;

$string =~ s/(.{1,4})/$chunkmap{$1}/g;
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