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#!/usr/bin/perl

...
    close(OUT);
}

146529  0.777314368326637
146529  0.777314368326637
146530  0.116241153901913
...
146532  -0.150051720847835
146533  0.037500790454267
146533  0.03750079045426

...
 foreach my $key (sort keys %ref){
        print OUT $ref{$key}."\t".$probes[$key];
...
    }

146542  2       31852
146542  2       31852
146543  2       37693
...
146546  2       41256
146547  2       43652
146547  2       43652