file1:
ATCGATGTGT
CCGATGCTGA
...

file2:
CCGATGCTGAggatgtcgcgcagatttaggCCGATGCTGAgagcatgaa...

##</code><code>##

  my $matched='';
        foreach (@probes){
                                chomp $_;
                                if ($chrom=~/$_/gi) {
                                my $position=pos($chrom);
                                $matched.= "$_\t$position\n";
                                }
         }