open INDAT, "file1" or die "$!";
my @array;
my @probes;
while (<INDAT>){
        @array=split/\t/;
        open INCOMP, "file2" or die "$!";
        while (<INCOMP>){
                @probes=split/\t/;

                if ($array[0]=~/$probes[1]/i){
                        print $probes[1];#or whatever else 
                        }
               }
         close INCOMP;
         }