private static void writeResults(List<Holder> list) throws Exception
	{
		BufferedWriter writer = new BufferedWriter(new FileWriter(
				new File(ConfigReader.getCREOrthologsDir() + File.separator + 
				"gatheredKmerMatrices" + File.separator + "comparison_700000"
						+ ".txt")));
		
		writer.write("name1\tname2\tallDist\tsubDist\tbothPneu\n");
		
		int firstIndex=0;
		int secondIndex =0;
		
		List<String> names = getNames();
		
		for( Holder h : list)
		{
			if( firstIndex < secondIndex)
			{
				writer.write( getThreeTokens(names.get(firstIndex)) + "\t" + getThreeTokens(names.get(secondIndex)) + "\t");
				
				writer.write( h.dist1  + "\t" + h.dist2 + "\t");
				
				writer.write( (names.get(firstIndex).indexOf("pneu") != -1 &&  
						names.get(secondIndex).indexOf("pneu") != -1)  + "\n");
			}			
			
			firstIndex++;
			
			if( firstIndex == names.size())
			{
				firstIndex = 0;
				secondIndex++;
				System.out.println(secondIndex);
			}
		}
		
		writer.flush();  writer.close();
		
		if( firstIndex != 0)
			throw new Exception("no " + firstIndex);
		
		if( secondIndex != names.size())
			throw new Exception("No " + secondIndex);
		
		
	}