use warnings;
use strict; 

open( F1, "subsettest.txt" ) or die "file1: $!";
open( F2, "subsettest1.txt" ) or die "file2: $!";

while ( my $s1 = <F1> ) {
   my $s2 = <F2>;
   if ( $s1 =~ /^>/ ) {
      print $s1;
   } else {
      print $s2,$s1;  
   }
}
close F1;
close F2;
exit;