use strict;
use warnings;

my @instances = qw ( 
                     AAAAA
                     ATCGA
                     ATAAA
                 );
my @instances2 = qw ( 
                     AAAAA
                     AACGA
                     ATAAA
                     ATAAA
                 );

print consensus(@instances),"\n";

sub consensus{
 my @mi = @_;
 my $motif_count=0;
 my @words =();
 my $L = undef;

  my  @A = ();
  my  @T = ();
  my  @C = ();
  my  @G = ();

  my  $a = 0;
  my  $c = 0;
  my  $g = 0;
  my  $t = 0;
  my  $w = 0;

	foreach my $mi ( @mi ) {
        chomp($mi);
        $mi =~ s/\s//g;

		$w = length($mi);

        #for motif instances count
        @words = split( /\W+/, $mi );
        $motif_count += @words;
      }

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

        # Initialize the base counts.
        my $L =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 );

        $a = 0;
		$c = 0;
		$g = 0;
		$t = 0;

    }

    my @cons = ();
    #print "$w\n";
    for (my $b=0; $b <$w ;$b++) {

		if ( $A[$b] > $T[$b] && $A[$b] > $C[$b] && $A[$b] > $G[$b] ) {
            push( @cons, 'A');
        }

        elsif ( $T[$b] > $C[$b] && 
                $T[$b] > $A[$b] && 
                $T[$b] > $G[$b] ) {
            push( @cons, 'T' );
        }

        elsif ( $C[$b] > $G[$b] && 
                $C[$b] > $A[$b] && 
                $C[$b] > $T[$b] ) {
            push( @cons, 'C' );
        }
	  elsif ( $G[$b] > $A[$b] && 
                $G[$b] > $C[$b] && 
                $G[$b] > $T[$b] ) {
            push( @cons, 'G' );
        }
		elsif ( $A[$b] = $T[$b] ) {
            push( @cons, 'T' );
        }
		elsif ( $A[$b] = $G[$b] ) {
            push( @cons, 'G' );
        }
		elsif ( $A[$b] = $C[$b] ) {
            push( @cons, 'C' );
        }
		elsif ( $T[$b] = $C[$b] ) {
            push( @cons, 'C' );
        }
		elsif ( $T[$b] = $G[$b] ) {
            push( @cons, 'G' );
        }
		else { push @cons, 'G'; }


    }

	return @cons;
}