try this

#!/usr/bin/perl
use warnings;
use strict;

my %bow1 = ();
my $file1 = shift;
open (FILE1, "$file1")or die "could not open FILE1:$file1; # Open firs
+t file

while (<FILE1>) {
    my ($ID1, undef, undef, undef, $Seq1) = split;
    $bow1{$ID1} = $ID1; # your id is the key and can be got again
}
close FILE1;

my $file2 = shift;
open (FILE2, "$file2")or die "could not open FILE2:$file2"; # Open sec
+ond file

while (<FILE2>) {
    my ($ID2, undef, undef, undef, $Seq2) = split;
    if(defined($bow1{$ID2})){#IDs Match
       if($bow1{$ID2} eq $Seq2){
               #both match so remove from the hash to avoid looking fo
+r a correct one later
               delete $bow1{$ID2};
       }else{
       #id's dont match
       print "IDs exist but dont match ID:$ID2:Seq1:$bow1{$ID2}:Seq2:$
+Seq2:\n";
       }
    }else{
        #id not in list 1
        print "ID only in file 2 ID:$ID2:$Seq1\n"
    }   
}
close FILE2
#run through any remaing list one items that werent matched
while((my $key,my $value) = each %bow1){
    print "ID only in file 1 ID:$key:Seq:$value:\n";
}
[download]