while(<FILE>){
    $_=~s/\s+//g;
    push(@array1,$_);
}
my %s = ();
$s{$_}++ for @array1;

##</code><code>##

N01A0000.fBG1_c22
N01A000X.fBG1_c5
N01A000X.rBG1_c5
...

##</code><code>##

my %s;
while(<FILE>) {
    s/\s+//g;
    $s{$_}++;
}