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for my $pattern (@array2) {
    my @results = grep /$pattern/, @array1;
    print "$pattern is in @results\n";
}

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abc_RCF_BM_allocation_0_kl contains BM_allocation_0
abc_RCF_BM_allocation_0_kl contains RCF_BM_allocation_0
aplc_RCF_BM_allocation_0_in_nml contains RCF_BM_allocation_0_in
aplc_RCF_BM_allocation_0_in_nml contains BM_allocation_0