#!/usr/bin/perl 
use warnings; 
 $a=">gi1 cds
ATG fun 
>gi2 cds
ATG fun
>gi3 cds
GGG fun";        
 while ($a=~ m/(>.*?fun)/gs) { $b1=$&;  $b2=$&;   
      while ($b1=~ />.*?cds/gs) { $h=$&; 
             $b2=~ s/$h//g; $b2=~ s/fun//g; 
             $seq=$b2; $seq=~ s/\n//;
         $hdr_seq="$h\n"."$seq\n"; 
        push @hdr_seq1,$hdr_seq; 
        push @only_seq1,$seq;             
      }   
   }  
# To remove multiple copies (if any): 
   my %seen; # declare a hash 
 my @only_seq=(); my @hdr_seq=();    
 @only_seq=grep{!$seen{$_}++}@only_seq1;   
 @hdr_seq=grep{!$seen{$_}++}@hdr_seq1; 
print "\n\n A. Header & sequences are:\n\n"; 
print join ("\n", @hdr_seq); 
print "\n"; 

print "\n B. Only sequences are:\n\n";  
print join ("\n", @only_seq); 
print "\n\n";   
                $num=0; 
 foreach my $item1 (@only_seq) {$num++; # No.1 curly
         $seq1=$item1;           
   foreach my $item2 (@hdr_seq) {       # No.2 curly  
     if (defined $item2) { $item2=$item2;  $item3=$item2;}    
       while ($item2=~ m/>.*cds/gs) { $hdr2=$&;              
            $item3=~ s/$hdr2//; $item3=~ s/\s//; 
            $seq2=$item3;
            $ele2="$hdr2\n"."$seq2\n"; 
           if ($seq1 eq $seq2) {push @result1,$ele2;} 
           else {push @result1,$ele2;} 
        } 
    } # No.2 curly              
  } # No.1 curly  
######################################
 my @result=(); 
 @result=grep{!$seen{$_}++}@result1;    
print "\n C. Non-redundant sequences are:\n\n"; 
print join ("",@result); 
print "\n"; 
exit;  

##</code><code>##

Microsoft Windows [Version 6.1.7600]
Copyright (c) 2009 Microsoft Corporation.  All rights reserved.
C:\Users\x\Desktop>try.pl
 A. Header & sequences are:
>gi1 cds
ATG
>gi2 cds
ATG
>gi3 cds
GGG
 B. Only sequences are:
ATG
GGG
C.  Non-redundant sequences are: (This is wrong) 
>gi1 cds
ATG
>gi2 cds
ATG
>gi3 cds
GGG 

##</code><code>##

>gi1 cds
ATG
>gi3 cds
GGG