Firstly, you slurp the entire file into memory with the line that reads @file = <FILE>;. Secondly, you loop over each line of the file many many times. Also, not relating to your problem per se, but you are using an array that contains a single array reference and it doesn't look like there's any reason for that (@ranges will always have one element, the reference to your 4 values. Similar for @range_counts since it's built from @ranges).