A couple of pointers and maybe then you can clarify what you want to achieve

• Your program declares a @arr variable but never uses it. Please try to post the smallest code possible that exhibits your problem.
• You are saying that you are saving each line of the file in a separate array. That is not the case. You are overwriting scalar variables (like $entry or $title) each time you encounter a matching line. So e.g. at the end of your loop, you have the last ORGANISM line in the scalar variable $org.
• You are reading through your file line by line. How do you expect the 2nd line of a title to end up in the $title variable? None of your regular expressions match on this 2nd line so the else brach is executed and this line is pushed onto the array @se.