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    if ($SIRtrue && !($_ =~ /SPECint_base/)){
    $SIR{$_}=$_;
    }
    if ($SFRtrue && !($_ =~ /SPECfp_base/)){
    $SFR{$_}=$_;
    }

use strict;
use warnings;

...

print Dumper(\%SIR);
print Dumper(\%SFR);

$VAR1 = {
          'SPECint_base' => [
                              '1',
...
                             '6'
                           ]
        };