# Remove extraneous characters, make it one big long string to use sub
+str position on it
$genome =~ s/[\d\r\n\s]+//g;
[download]

The \s character class includes the characters \r and \n so including them is superfluous. If you want efficiency then use tr/// instead of s///:

# Remove extraneous characters, make it one big long string to use sub
+str position on it
$genome =~ tr/0-9 \t\f\n\r//d;
[download]