If it's only that simple kind of problem that you mentioned (find one string in another string), then Ikegami's solution (index) should suffice. If you need to do that by regex, try:

  ...
  my $str1 = 'AT1G7. +126[0]*';
  my $str2 = 'AT1G7. +126[0]*_|_chr1';
  ...
  (my $results) = $str2 =~ /\Q$str1/g;
  print $results if $results;
  ...
[download]

Regards

mwa