There's no need to use regex for most of that, since you aren't searching case insensitive anyway.

use strict;
use warnings;

my ($features, $count, @seq);
while (<DATA>) {
    if (index($_, 'FEATURES') != -1) {
        ($features) = m/\s(\S+)/;
    }
    elsif (index($_, 'COUNT') != -1)   {
        ($count) = m/\s(\d+)/;
    }
    elsif (index($_, 'ORIGIN') != -1) {
        push @seq, $_ until index($_ = <DATA>, '//') != -1;
    }
}
print "$features\n$count\n",@seq;


__DATA__
# extract of file:  
#===============

FEATURES             Location/Qualifiers    
                     /note="blah blah"   
COUNT                200
ORIGIN
        1 lots of nice info
       61 lots of nice info
      121 lots of nice info
   
//
[download]