compare Cx clustal

#!/usr/bin/perl
#compare Cx clustal
#
# VR
#
#


open (SEKOS, "sulygintos.clustal") or die ("Could not open $ARGV[0].\n");
foreach $line (<SEKOS>)  {
        chop($line);
        push @Cx26_seka, split(/      /, $line) if ($line =~ "P29033");
        push @Cx30_2_seka, split(/      /, $line) if ($line =~ "Q8NFK1");
        push @Cx36_seka, split(/      /, $line) if ($line =~ "Q9UKL4");
        push @Cx40_seka, split(/      /, $line) if ($line =~ "P36382");
        push @Cx43_seka, split(/      /, $line) if ($line =~ "P17302");
        push @Cx45_seka, split(/      /, $line) if ($line =~ "P36383");
        push @Cx46_seka, split(/      /, $line) if ($line =~ "Q9Y6H8");
        push @Cx47_seka, split(/      /, $line) if ($line =~ "Q5T442");
        push @Cx50_seka, split(/      /, $line) if ($line =~ "P48165");
}
close(SEKOS);


@Cx26_seka = grep !/sp/, @Cx26_seka;
@Cx30_2_seka = grep !/sp/, @Cx30_2_seka;
@Cx36_seka = grep !/sp/, @Cx36_seka;
@Cx40_seka = grep !/sp/, @Cx40_seka;
@Cx43_seka = grep !/sp/, @Cx43_seka;
@Cx45_seka = grep !/sp/, @Cx45_seka;
@Cx46_seka = grep !/sp/, @Cx46_seka;
@Cx47_seka = grep !/sp/, @Cx47_seka;
@Cx50_seka = grep !/sp/, @Cx50_seka;


$Cx26 = join("", @Cx26_seka);
$Cx30_2 = join("", @Cx30_2_seka);
$Cx36 = join("", @Cx36_seka);
$Cx40 = join("", @Cx40_seka);
$Cx43 = join("", @Cx43_seka);
$Cx45 = join("", @Cx45_seka);
$Cx46 = join("", @Cx46_seka);
$Cx47 = join("", @Cx47_seka);
$Cx50 = join("", @Cx50_seka);


@ar_Cx26 = split(//, $Cx26);
@ar_Cx30_2 = split(//, $Cx30_2);
@ar_Cx36 = split(//, $Cx36);
@ar_Cx40 = split(//, $Cx40);
@ar_Cx43 = split(//, $Cx43);
@ar_Cx45 = split(//, $Cx45);
@ar_Cx46 = split(//, $Cx46);
@ar_Cx47 = split(//, $Cx47);
@ar_Cx50 = split(//, $Cx50);

#print join("\n", @ar_Cx50);

$count = 0;
while ($ar_Cx26[$count]) {
                if (
                $ar_Cx26[$count] eq $ar_Cx40[$count] &&
                $ar_Cx26[$count] eq $ar_Cx46[$count] &&
                $ar_Cx26[$count] eq $ar_Cx47[$count] &&
                $ar_Cx26[$count] eq $ar_Cx50[$count] &&
                $ar_Cx26[$count] ne $ar_Cx30_2[$count] &&
                $ar_Cx26[$count] ne $ar_Cx36[$count] &&
                #$ar_Cx26[$count] ne $ar_Cx43[$count] &&
                $ar_Cx26[$count] ne $ar_Cx45[$count]
                )       {
                                print $count+1, " : ";
                                print $ar_Cx26[$count];
                                print "\n";
                        }
                $count++;
        }