$string_filename = 'sequence.txt';  

open(FILE, $string_filename) || die("Couldn't read file $string_filename\n");

$motif_filename = 'motif.txt';   

open(MOTIF, $motif_filename) || die("Couldn't read file $motif_filename\n"); 

local $/ = "\n>";  

   while (my $seq = <FILE>) {
chomp $seq;
$seq =~ s/^>*.+\n//;  
$seq =~ s/\n//g;  

$R = length $seq;  
  $motif = <MOTIF>; 
chomp $motif;
$motif =~ s/^>*.+\n//; 
$motif =~ s/\n//g; 
  if ( $seq =~ /$motif/ ) {     ## insert actual binding site 
    $M = $';
    $W = length $M;

    if ( $seq =~ /[A-Z]/) {    ##  exon start
        $K = $`;   
        $Z = length $K;  
        $x = $W + $Z - $R;     
        print "\n\ the distance is the following: $x\n\n";

    } else {  
        print "\n\ I couldn't find the start codon.\n\n";
    }
} else {  
    print "\n\ I couldn't find the binding site.\n\n";   
}

}

close MOTIF;   
close FILE;   

exit;