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use warnings;
use strict;
...
$VAR1 = 'ux_prim_clk';
$VAR2 = 'ux_side_clk';
$VAR3 = 'ux_xtal_frm_refclk';

use warnings;
use strict;
...
my @clk_new = map{my $line =join ("_", @$_); $line}@clk_output;

print Dumper \@clk_new;