Better?

#! perl -slw
use strict;
use Data::Dumper;

sub get_pwm {
    my @data = @_;

    my $l = length( $data[0] );
    my %pwm = map{ $_ => [ (0) x length( $_[ 0 ] ) ] } qw[ A C G  T ];
    foreach my $line (@data) {
        ++$pwm{ substr $line, $_, 1 }[$_] for 0 .. $l - 1;
    }
    my $n = @data;
    @$_ = map { $_ ? $_ / $n : 0 } @{ $_ }[ 0 .. $l - 1 ]  for values 
+%pwm;

    return \%pwm;
}

my @inst = (
    'GGTGTGCC',
    'GCTGTGGG',
    'GGTGGGCC'
);

my $res = get_pwm(@inst);

printf "%1s => [ %s ]\n", $_ => join ' ', map{
        sprintf '%5.2f', $_
    } @{ $res->{ $_ } } for keys %{ $res };

__END__
c:\test>530623.pl
A => [  0.00  0.00  0.00  0.00  0.00  0.00  0.00  0.00 ]
T => [  0.00  0.00  1.00  0.00  0.67  0.00  0.00  0.00 ]
C => [  0.00  0.33  0.00  0.00  0.00  0.00  0.67  0.67 ]
G => [  1.00  0.67  0.00  1.00  0.33  1.00  0.33  0.33 ]
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