use warnings; open AS, "data"; open AQ, "pattern.txt"; @arr=; @arr1=; foreach $line(@arr) { @split=split(' ',$line); foreach $line1(@arr1) { @split1=split(' ',$line1); if($split[0] eq $split1[0] && $split[1] eq $split1[1]) { print $split1[0],"\t",$split1[1],"\t",$split1[3],"\n";} } } close AQ; close AS;