Can you explain how you derive the matrix values in your result, given the sample input? It's unclear how you are parsing input to get to that matrix.

So far as I can tell, the "similar question" is in fact identical to this one. So this one should be closed.

I agree--same question as before.

I am sorry, but it is not our problem that you cannot figure out how to edit your question. Also, I have asked the user before to avoid putting stuff on this good<dot>gd and use a different service, (one that doesn't include flashy porn ads to host a zip file, and that most people will able to read) for example pastebin. I might want to put a ban on the user for reapeatedly ignoring this.

Just for the fun (thanks to matted for pointing the modification):

#!/usr/bin/perl

use strict;
use warnings;

my %motifs;
my @files = @ARGV;

foreach my $file (@files) {
    open F, "$file" or die;
    my $n = 0;
    while (<F>) {
        chomp;
        if (m/>.+x(\d+)/ { $n = $1; }
        else { $motifs{$_}{$file} += $n; }
    }
    close F;
}

print join "\t", 'motif', @files;
print "\n";
foreach my $motif (sort keys %motifs) {
    print "$motif";
    foreach my $file (@files) {
        my $cnt = 0;
        $cnt = $motifs{$motif}{$file} if (defined $motifs{$motif}{$file});
        print "\t$cnt";
    }
    print "\n";
}