my %seen;
for ( reverse <DATA> ) {
  ( my $unstarred = $_ ) =~ s/\*\*/  /;
  print unless $seen{ $unstarred }++;
}

__DATA__
30380868    N Sep 29               356200        AGEC682569   ATI     
+  S
30380868 ** N Sep 29               356200        AGEC682569   ATI     
+  S
71130740    N Sep  7               SM9481        AGEC683966   ATI     
+  S
71130740 ** N Sep  7               SM9481        AGEC683966   ATI     
+  S
32450045    N Jul 14               SN9672        AGEC685203   ATI     
+  S
32450045 ** N Jul 14               SN9672        AGEC685203   ATI     
+  S
36450223    N Aug 30               SU8329        AGEC685348   ATI     
+  S
34680135    N Sep 30               349450        AGEC685442   ATI     
+  S

[download]

The only difference from your 'desired output' is that this code prints it out in reverse order. But I don't see this as a problem, as there seems to be no inherent order in the input/output anyway...

In reply to Re^3: Selective printing of the Duplicates by Not_a_Number
in thread Selective printing of the Duplicates by Thomas Kennll

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