#!/usr/bin/perl 
use warnings; 
use strict;  

my $a=">sample1 ..sequence
ATGC fun
>sample2 ..sequence
ATGC fun
>sample3 ..sequence
CCGG fun
>sample4 ..sequence
CCGG fun"; 

 while ($a=~ />.*?fun/gs) {my $trial1=$&; my $trial2=$&;     

    while ($trial1=~ />.*sequence/gs) {my $header=$&;  
           $trial2=~ s/($header)//gs; 
           my $seq=$trial2; 
           $seq=~ s/\s//;
           $seq=~ s/fun//;   

    print "\n Header: $header
 Sequence: $seq\n"; 
    } 
 } 
# code?? 
exit;

##</code><code>##

 C:\Users\x\Desktop>t2.pl

 Header: >sample1 ..sequence
 Sequence: ATGC

 Header: >sample2 ..sequence
 Sequence: ATGC

 Header: >sample3 ..sequence
 Sequence: CCGG

 Header: >sample4 ..sequence
 Sequence: CCGG 

##</code><code>##

>sample1 ..sequence
ATGC
>sample3 ..sequence
CCGG