### CREATE TWO SAMPLE DNA SEQUENCES ###
@nucleotides=('A','T','G','C');
foreach(1..1000)
	{
	$seq1.=$nucleotides[int(rand(3))];
	}
foreach(1..1000)
	{
	$seq2.=$nucleotides[int(rand(3))];
	}


### SETTINGS FOR THE DOTPLOT ###
$window_size=5;
$max_mismatch=1;


@seq1=split('',$seq1);
foreach(1..$window_size)
	{
	shift@seq1;
	}
@seq2=split('',$seq2);
foreach(1..$window_size)
	{
	shift@seq2;
	}

open(OUT,">ID_matrix.txt");
$number_of_windows_1=((length$seq1)-$window_size)+1;
$number_of_windows_2=((length$seq2)-$window_size)+1;

$time_start=time;
foreach$window_no(0..$number_of_windows_1-1)
	{
	@seq2_temp=@seq2;
	if($window_no==0)
		{
		$current_window=substr($seq1,0,$window_size);
		@current_window=split('',$current_window);
		}
	else
		{
		shift@current_window;
		$next_character=shift@seq1;
		push(@current_window,$next_character);
		}
	foreach$query_no(0..$number_of_windows_2-1)
		{
		if($query_no==0)
			{
			$query_window=substr($seq2,0,$window_size);
			@query_window=split('',$query_window);
			}
		else
			{
			shift@query_window;
			$next_character=shift@seq2_temp;
			push(@query_window,$next_character);
			}
		$count_matches=0;
		foreach(0..$window_size-1)
			{
			if($current_window[$_]eq$query_window[$_])
				{
				$count_matches++;
				last if($_-$count_matches>$max_mismatch);
				}
			}
		if($count_matches>=$window_size-$max_mismatch)
			{
			print OUT "1";
			}
		else
			{
			print OUT "0";
			}
		}
	print OUT"\n";
	}
$time_end=time;
$time_used=$time_end-$time_start;
close OUT;
print"Time used: $time_used seconds.\n";
system("pause");
exit;