while(<F1>) { # this is the "Biiiiigggg Sequence"
	$targetseq = $_;
	print "$targetseq\n";
	chomp($targetseq);
	open(F2,"<$file2") or die "Error opening $file2: $!";
	while(<F2>) { # probe sequences (25 base)
	   substr($_,0, 25);
	   $probe = $_;
	   chomp($probe);
	   if ($targetseq=~ /.*$probe.*/) { *this is Line 29
	      $start = index($targetseq, $probe);
	      push(@matchregion,$start);
	   }
	}	
	$indexes = @matchregion;