You could compress the sequences (substrings) into vectors like so:

my $bitvec = pack "H*", ($string =~ tr/AGCT/1248/r);
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Convert the bitvectors into integer vectors and sum them up. Better yet and if memory allows, create one big vector from the full sequence (with 4*length elements), as the first step.

Then, using an appropriate module with overloading, you might simply (completely untested code):

my @arrr = split //, unpack "B*", $bitvec;
my $histogram = Math::GSL::Vector->new();
my $sequence = Math::GSL::Vector->new( \@arrr );

while (($pos,$freq) = each %points) {
    my $view = gsl_vector_subvector( $sequence, 4 * $pos, 4 * $slen );

    $histogram += $view * $freq;
    $sum_freq += $freq;
}

# normalize and uninterleave
$histogram *= 1 / $sum_freq;
@parts = part { $i++ % 4 } $histogram->as_list;
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