my $alt = join '|', reverse sort <$matches_fh>;
my $re = qr{(?x: ^ > ( $alt ) )};
my %count;
/$re/ && ++$count{$1} while <$fasta_fh>;

##</code><code>##

#!/usr/bin/env perl

use strict;
use warnings;

use Data::Dump;
use Inline::Files;

my $alt = join '|', reverse sort <MATCHES>;
my $re = qr{(?x: ^ > ( $alt ) )};
my %count;
/$re/ && ++$count{$1} while <FASTA>;

dd \%count;

__MATCHES__
Gloin1
XYZ1
XYZ
XYZ12
__FASTA__
>Gloin1_1
unwanted data
>XYZ_1
unwanted data
>XYZ12_1
unwanted data
>XYZ1_2
unwanted data
>XYZ1_1
unwanted data
>XYZ12_3
unwanted data
>Gloin1_2
unwanted data
>XYZ12_2
unwanted data

##</code><code>##

{ Gloin1 => 2, XYZ => 1, XYZ1 => 2, XYZ12 => 3 }