An input record separator (found in Perl's variable $/ and usually set to \n) determines the end of a line ('record') when reading from a file--like you were doing in your while loop. It's kept on the end of the line, unless you do something like chomping the line. In your case, not removing the input record separator produced undesirable results in your final output. (Sometimes, however, the very last line of a file may not terminate with an input record separator, because the line ends at the end of the file.)