Security in Cyber-Physical Systems (CPS) has become a serious concern owing to the rapid adoption of technologies such as plug-and-play connectivity, robotics and remote coordination and control. It is well understood that the performance overhead incurred due to security considerations is rather high, which needs to be captured holistically for a real-time CPS with strict timing budget and hard deadlines. Additionally, attacks in real-time CPS may only alter the timing behaviour of system components without any changes in functionality, resulting in serious consequences due to missed deadlines. To address this challenging issue, it is necessary to understand the role of diverse components in a real-time CPS and how those expose the system to a malicious attacker. In this paper, we propose a systematic security analysis flow, using a novel Attack Sequence Diagram (ASD), which links the sources, intermediate components and final manifestations of an attack, thereby clearly delineating the attack surfaces of a complex real-time CPS. Based on the ASD, it is possible to evaluate the complexity of an attack, performance overhead of a countermeasure and explore different design trade-offs for a realtime CPS. With the help of real-world and synthetic examples, we demonstrate that ASD seamlessly enables one to map the existing vulnerabilities and uncover new attack possibilities.