Hi natoikos,

I don't know if this would be helpful for you or not,
but after playing with your code and some example files,
I wonder if you are searching for multiple matches of $array[0] in your $probes1 list in file2,
or after finding the first match of $array[0], you want to move on to the next $array[0] and continue searching.
But I think the while loop quits running after finding the first match.
Perhaps you want to use a different loop structure.
Saints, please correct me if I am wrong.