Something along these lines then:

use strict;
use warnings;

my $inputFile = q{/path/to/NRT2.txt};
open my $inputFH, q{<}, $inputFile
   or die qq{open: < $inputFile: $!\n};

my %occurs;
while ( <$inputFH> )
{
    $occurs{ $1 } ++ if m{^>([^_]+)}
}

close $inputFH
   or die qq{close: < $inputFile: $!\n};

print qq{$_: $occurs{ $_ } occurrences in $inputFile\n}
   for sort keys %occurs;

[download]

A more comprehensive example of your input file would be needed to be sure of the solution.

Update: Too simplistic, ignore this as examples of both files are needed before making a stab at a solution.

Cheers,

JohnGG

In reply to Re^3: Counting matches by johngg
in thread Counting matches by Nicpetbio23!

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