Step 1: What exactly is it you don't like? (CRLF in the middle of your print)
Step 2: Where in the code does it do that? (Somewhere between printing the text of the line and printing the IN or OUT, conveniently, this is on the same line so you don't have to look very far.)
Step 3: Consider what it is doing there. Add debug prints to make clear what your variables are at that point. (There's a \n before your \tIN... and the $column[$number] is the thing before the \t... print "-=)$column[$number](=-";? Well, that will prove that you've got a CRLF in there.)
Step 4: Understand. The CRLF is in your string because every line of your file ends with a CRLF, of course!
Step 5: Fix it. chomp was made for this.