use strict;
use warnings;

my $File1 = <<END_FILE1;
GP_MASA_38C02_c
GP_MASA_33B06_c
GP_MASA_24D04_c
GP_MASA_35A04_c
END_FILE1

my $File2 = <<END_FILE2;
'GP_MASA_01F04_c',681,'ACCACACATCATCTGACTTACGTACGTACG......
'GP_MASA_38C02_c',273,'ACATCCTTCACAGAAGTTTGT.............
'GP_MASA_33B06_c',288,'ACATACTAACACGGTCTTT...............
END_FILE2

my $match = 0;

open my $dataIn, '<', \$File2;

while (<$dataIn>) {
    chomp ($_);
    my $dataLine = $_;

    open my $refIn, '<', \$File1;

    while (<$refIn>) {
        chomp ($_);
        my $str = $_;
        if ($dataLine =~ /$str/) {
            $match = 1;
        }
    }
    close ($refIn);
    if ($match == 0) {
        print "$dataLine\n";

    }
    $match = 0;
}

##</code><code>##

'GP_MASA_01F04_c',681,'ACCACACATCATCTGACTTACGTACGTACG......