#!/usr/bin/perl
{
  local $/ = "INPUT SEQUENCE=";
  <>; # discard first chunk
  while(<>) {
    chomp;
    open O, '>', /^(\d+)/ and $1 or die "$!\n";
    print O $/,$_;
  }
}

##</code><code>##

#!/usr/bin/perl
{
  my $file = 'File00000';
  local $/ = "INPUT SEQUENCE=";
  <>;
  while(<>) {
    chomp;
    unless ($.-2 % 1000) {
        open O, '>', ++$file or die "cant write '$file': $!\n";
    }
    print O $/,$_;
  }
}