AAA
                    ATG
                    TTT
                    GTC

Note that the length of these strings in the set 
maybe greater than 3. 

##</code><code>##

$VAR1 =  {
            'A' => [2,1,1],
            'T' => [1,3,1],
            'C' => [0,0,1],
            'G' => [1,0,1]
         };

So the size of the array is the same with the length of the string.

In my case I need the variation of it, namely the probability of the 
each base occur in the particular position:
$VAR =     {
            'A' => ['0.5','0.25','0.25'],
            'T' => ['0.25','0.75','0.25'],
            'C' => ['0','0','0.25'],
            'G' => ['0.25','0','0.25']
          }


##</code><code>##

#!/usr/bin/perl -w
use strict;
use Data::Dumper;
use Carp;

my @Array = ('AAA',
             'ATG',
             'TTT',
             'GTC');

my ($PWM) = compute_pwm(@Array);


print Dumper $PWM;


#The code that does the job

sub compute_pwm {
    my @mi = @_;
    my $motif_count;
    my $L;

    #-------Beginning of PWM processing ----------------
    foreach my $mi (@mi) {
        chomp($mi);
        $mi =~ s/\s//g;
        $L = $mi;

        my @words = split( /\W+/, $mi );
        $motif_count += @words;
    }
    $motif_count = 0;

    my $w = length($L);
    my @A = ();
    my @T = ();
    my @C = ();
    my @G = ();

    for ( my $j = 0; $j < $w; $j++ ) {

        # Initialize the base counts.
        my $a = 0;
        my $c = 0;
        my $g = 0;
        my $t = 0;

        foreach my $mi (@mi) {
            chomp($mi);
            my $L = $mi;
            my $sb = substr( $L, $j, 1 );
            while ( $sb =~ /a/ig ) { $a++ }
            while ( $sb =~ /t/ig ) { $t++ }
            while ( $sb =~ /c/ig ) { $c++ }
            while ( $sb =~ /g/ig ) { $g++ }

        }
        push( @A, $a );
        push( @T, $t );
        push( @C, $c );
        push( @G, $g );
    }

    my $sumA = sumArray(@A);
    my $sumT = sumArray(@T);
    my $sumC = sumArray(@C);
    my $sumG = sumArray(@G);

    my @m    = ();
    my @Anm1 = ();
    my @Tnm1 = ();
    my @Cnm1 = ();
    my @Gnm1 = ();
    my @sPos = ();

    #summing up A,T,C,G for all position
    for ( my $b = 0; $b < $w; $b++ ) {
        my $sumPos = $A[$b] + $T[$b] + $C[$b] + $G[$b];
        push( @sPos, $sumPos );

        my $nm1A = $A[$b]/$sumPos;
        my $nm1T = $T[$b]/$sumPos;
        my $nm1C = $C[$b]/$sumPos;
        my $nm1G = $G[$b]/$sumPos;

        push( @Anm1, $nm1A );
        push( @Tnm1, $nm1T );
        push( @Cnm1, $nm1C );
        push( @Gnm1, $nm1G );
    }

    my @PWM = pwm( \@Anm1, \@Tnm1, \@Cnm1, \@Gnm1 );
    return \@PWM;

}




#--------------- Subs of the subroutines ----------------------------

sub pwm {
    #PWM in forms of AoH
    
     my ($A,$T,$C,$G) = @_; #input are array references
     my (%Ah,%Th,%Ch,%Gh);

     $Ah{'A'} = [@$A];
     $Th{'T'} = [@$T];
     $Ch{'C'} = [@$C];
     $Gh{'G'} = [@$G];

     my @PWM; #AoH
     push @PWM, {%Ah,%Th,%Ch,%Gh};

     return @PWM;
}

sub sumArray
{
  my @arr = @_;
  my $sum = 0;
  my $count = $#arr + 1;
  for(my $i=0;$i<$count;$i++){
     $sum += $arr[$i];
  }
  return $sum;
}