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# use strict;

my(@folder_name,$temp1,$temp2);
...
$temp1 = <ONE>;
...
$temp2 = <TWO>;

mkdir "/var/www/html/piRNA_html/UNAFold/output/$temp2",0777
  or die "Cannot make directory /var/www/html/piRNA_html/UNAFold/outpu
+t/$temp2, error was $!";