@seqss = split ('',$seq);
$m=scalar @seqss;
#FINDING OUT THE FIRST AND THE LAST CHARACTER OF THE MOTIF
$firstch=$seqss[0];
$lastch=$seqss[$m-1];

would be better written as

@seqss = split ('',$seq);
#FINDING OUT THE FIRST AND THE LAST CHARACTER OF THE MOTIF
$firstch=$seqss[0];
$lastch=$seqss[-1];

##</code><code>##

@pats=reverse @seqss;
foreach my $elem ( @pats )
{
next if $seen{ $elem }++;
push @uni, $elem;
@unique= reverse @uni;
}

##</code><code>##

for(my $i=0;$i<scalar @unique;$i++) {
  $mcut=scalar @unique;
  $m=$mcut-$i;
  %num=("$unique[$i]"=>"$m");
  while (($key1, $val1) = each(%num)) {
    push(@key,$key1);
    push(@val,$val1);
  }
}