Use a frickin hash!

use strict;
use warnings;

my @gl = qw(
    CD9
    TBN
    NANOG
    KITL
    FUT4
    SALL4
    MYC
    STAT3
    ESRRB
    AKP2
    SOX2
    POU5F1
    KLF4
);

my @hfr_genes = qw(
    LYPLA1
    LYPLA1
    LYPLA1
    LYPLA1
    STAT3
    LYPLA1
    LYPLA1
    STAT3
    LYPLA1
    LYPLA1
    LYPLA1
    LYPLA1
    SOX2
);

# First thing: convert @hfr_genes into a hash!!!
# Looking up a hash key is much faster than grepping an array.
my %hfr_genes;
$hfr_genes{$_}++ for @hfr_genes;

# Now loop through the first list
for (@gl) {
    my $count = $hfr_genes{$_};
    print "Value $_ is present $count times\n" if $count;
}
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