Hi natoikos, Use chomp after reading a line from the files.

Try this,

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

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