while (traceTwo > 0 && traceOne > 0)
	{
	int diag = 0;


	if (seqTwoArray[traceTwo - 1] == seqOneArray[traceOne - 1])
	diag = 3;
	else
	diag = -1;

	//Chck if diagnonal is best path

	if (traceTwo > 0 && traceOne > 0 && scoringMatrix[traceTwo][traceOne] == scoringMatrix[traceTwo - 1][traceOne - 1] + diag)
	{

	AlignmentA = seqOneArray[traceOne - 1] + AlignmentA;
	AlignmentB = seqTwoArray[traceTwo - 1] + AlignmentB;
	traceTwo = traceTwo - 1;
	traceOne = traceOne - 1;


	}

	//Mismatch is best option
	else if (traceOne > 0 && scoringMatrix[traceTwo][traceOne] == scoringMatrix[traceTwo][traceOne - 1] - 4)
	{
	AlignmentA = seqOneArray[traceOne - 1] + AlignmentA;
	AlignmentB = "-" + AlignmentB;
	traceOne = traceOne - 1;

	}


	else if (traceTwo > 0 && scoringMatrix[traceTwo][traceOne] == scoringMatrix[traceTwo - 1][traceOne] -4)
	{
	AlignmentA = "-" + AlignmentA;
	AlignmentB = seqTwoArray[traceTwo - 1] + AlignmentB;
	traceTwo = traceTwo - 4;
	//cout << endl << AlignmentA << endl << AlignmentB << endl;

	}
	}

	cout << endl << AlignmentA << endl << AlignmentB << endl;