Regex used: /^$RE{num}{real}\s+(\d+)\s+\.\.\s+(\d+)\s*/

>hsa_circ_0075116|chr5:175956288-175956388-|NM_014901|RNF44  FORWARD
-4.6      12 ..      35   xxxxGTGTGTGGTCT          GC TTCAGTGACTTCGAGGCGCG GC           AGCTGCTCCGAGTCC
-5.5      11 ..      36   xxxxxGTGTGTGGTC         TGC TTCAGTGACTTCGAGGCGCG GCA          GCTGCTCCGAGTCCT

##</code><code>##

Dumper:
$VAR1 = 'hsa_circ_0075116|chr5:175956288-175956388-|NM_014901|RNF44  FORWARD';
$VAR2 = [
          {
            'end' => '35',
            'start' => '12'
          },
          {
            'end' => '36',
            'start' => '11'
          }

##</code><code>##

New regex: /^(\s+)?$RE{num}{real}\s+(\d+)\s+\.\.\s+(\d+)\s*/ 
 ## addition of (\s+)? to the beginning
*\s*-5      56 ..      70   CTATGCCCCTTATTG               TATCTG GGG CAGATG               ATCGTCAAGTGAAGA

##</code><code>##

$VAR125 = 'hsa_circ_0067224|chr3:128345575-128345675-|NM_002950|RPN1  FORWARD';
$VAR126 = [
            {
              'end' => '6',
              'start' => undef
            }

##</code><code>##

#!/usr/bin/perl 
use strict;
use warnings;
use Data::Dumper;
use Regexp::Common qw /number/;

open my $hairpin_file, '<', "new_xt_spacer_results.hairpin", or die $!;

my %HoA_sequences;
my $curkey;

while (<$hairpin_file>){
	chomp;
	
	if (/^>(\w+\d+\|\w+:\d+-\d+[-|+]\|\w+\|\w+\s+\w+$)/){
		$curkey = $1;

	}elsif (my ($start, $end) = 	
		/^(\s+)?$RE{num}{real}\s+(\d+)\s+\.\.\s+(\d+)\s*/ ) {

			die "value seen before header: '$_'"
				unless defined $curkey;
			push @{ $HoA_sequences{$curkey}}, 
				{ start=>$start, end=>$end };
	}
	else { die "don't know how to parse: '$_'" }
	
	
}
print Dumper(%HoA_sequences);