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#!/usr/bin/perl-w

#!/usr/bin/perl
use warnings;

open(my $outfile, ">", "Motif_Result.txt");

...

open(FIH, $patternseq);

open my $outfile, '>', 'Motif_Result.txt' or die "Cannot open 'Motif_R
+esult.txt' $!";

...

open FIH, '<', $patternseq or die "Cannot open '$patternseq' $!";

my $in;

...
         chomp($in);
         my @pats=split " ",$in;
         my $residue=shift@pats;

while ( <FIH> )
{
         my ( $residue, @pats ) = split;

         foreach my $nnn (@pats)  # @pats = (AAAAA, TTTTT, GGGGG);
         {
         $patsmap{$nnn}=@residue;
         }

         foreach my $nnn (@pats)  # @pats = (AAAAA, TTTTT, GGGGG);
         {
         $patsmap{$nnn} = 0;
         }

        print "Patterns\t"; print "@pats";             print "\n";
        my $length = @pats;
        print "Total Patterns are: $length"; print "\n";

        print "Patterns\t@pats\nTotal Patterns are: ", scalar @pats, "
+\n";

                 my @l = split('', $str);
                 my $length=@l;

                 my $length = length $str;

exit;
     }