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for($x=0; $x<3;$x++){
    for($y=0; $y<3;$y++){
        print $lines[$y][$x], " ";
    }
}

map {
    my $x=0;
...
    } @$_;

} @lines;

#!/usr/bin/perl
use CGI::Pretty qw(:standard);             # import CGI objects and fu
+nctions
...
   );

}