public Alignment getAlignmentScore() {
		int maxScore = Integer.MIN_VALUE;
		int xMax = 0;
		int yMax = 0;
		for (int i = 0; i < matrixA.length; i++) {
			if (matrixA[i][matrixA[i].length - 1] > maxScore) {
				maxScore = matrixA[i][matrixA[i].length - 1];
				xMax = i;
				yMax = matrixA[i].length-1;
			}
		}
		for (int j = 0; j < matrixA[0].length; j++) {
			if (matrixA[matrixA.length-1][j] > maxScore) {
				maxScore = matrixA[matrixA.length-1][j];
				xMax = matrixA.length-1;
				yMax = j;
			}
		}
		return new Alignment(maxScore / (double) submatrix.multiplicationFactor, xMax, yMax);
	}