Essentially what I wish to obtain is the starting position for each member of the @genes array within the original $screen variable.

I gave a solution using split in an earlier reply. I think I would prefer to solve this with a simple iterative regex, taking advantage of the @- array, which tracks the starting index of each sub-match:

  my @genes;
  my @gene_pos;
  while ( $screen =~ m/([^X]+)/g )
  {
      push @genes, $1;
      push @gene_pos, $-[1];
  }
[download]