if((defined $upstream_putative_TSD)&&(defined $downstream_putative_TSD))
            {
            # Check if the putative TSDs differ by just 1 mismatch or are perfect matches
                my $max_SNP = 1;
                my $diffCount = () = ( $upstream_putative_TSD ^ $downstream_putative_TSD ) =~ /[^\x00]/g;
                #                print $upstream_putative_TSD, "\t", $downstream_putative_TSD, "\t", $diffCount, "\n"; # OK thus far

                # syntax idea from https://www.biostars.org/p/83978/
                    if ($diffCount <= $max_SNP)
                    {
                        my $upstream_putative_TSD_non_canonical_letter_count = $upstream_putative_TSD =~ tr/BDEFHIJKLMNOPQRSUVWXYZ//;
                        # check to see whether upstream putative TSD contains anything but A/T/G/C, if yes, how many
                        my $downstream_putative_TSD_non_canonical_letter_count = $downstream_putative_TSD =~ tr/BDEFHIJKLMNOPQRSUVWXYZ//;
                        # check to see whether downstream putative TSD contains anything but A/T/G/C, if yes, how many
                            if(($upstream_putative_TSD_non_canonical_letter_count==0)&&($downstream_putative_TSD_non_canonical_letter_count==0))
                                {
                                    print $_, "\n";
                                    push @output, $_, "\n";
                                }
                    }
            }