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    while(<FILE>){
    $_=~s/\s+//g;
...
}
my %s = ();
$s{$_}++ for @array1;
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N01A000X.fBG1_c5
N01A000X.rBG1_c5
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  3. or download this
    my %s;
while(<FILE>) {
    s/\s+//g;
    $s{$_}++;
}