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for my $key ( keys %hash ) {
        if ( $key =~ /^dataS\d\dR\d$/ ) {
            print $key, @{ $hash{$key} }, "\n";
        }

my $first = 1;
for(my $i = 0; $i < $originalfilecount; $i++)
...
close $OUT3;

8899_Neg_Rep01_dataS01R01
8889_Neg_Rep02_dataS01R02
...
7709_Neg_Rep03_dataS05R03

(and so on...)