my @pat;
foreach my $r (@seq) {
   my $t = $r;
   $t =~ s/\h+/bbb/g;
   push @pat, [ $r, $t ];
}
while (<$fh>) {
   foreach my $p (@pat) {
      s/$p->[0]/$p->[1]/g;
   }
   print Newfile;
}