Try this

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

sub get_pwm {
    my @data = @_;

    my $l = length( $data[0] );
    my %pwm;
    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 = (
    'CAGGTG',
    'CAGGTG'
);

my $res = get_pwm(@inst);

print "$_ => @{ $res->{ $_ } }" for keys %{ $res };

__END__
c:\test>530623
A => 0 1 0 0 0 0
T => 0 0 0 0 1 0
C => 1 0 0 0 0 0
G => 0 0 1 1 0 1
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