my $Count = 0;
		foreach my $line (@file1){
			my ($chr, $start, $stop) = @$line;
			if ($chr eq $Chrom && $start gt $ModStart && $end lt $ModEnd){
				$Count++;
			}	
		}
		print ("$Gene\t$Chrom\t$ModStart\t$ModEnd\t$Strand\t$ExonCount\t$SizeKB\t$Count\n");