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Connected automated vehicles (CAVs) can significantly shorten the headway of car following, thereby effectively improving the traffic capacity and injecting new power to alleviate traffic congestion. To investigate the congestion characteristics of mixed traffic flow with CAVs and human-driven vehicles (HDVs), this paper proposes a cell transmission model to capture and simulate traffic congestion for mixed traffic flow. Firstly, the Newell, adaptive cruise control (ACC), and cooperative adaptive cruise control (CACC) models are adopted to capture the car-following behavior of different vehicles. Secondly, the fundamental diagram under different penetration rates of CAVs is derived based on car-following models. Then, the cell transmission model (CTM) of mixed traffic flow is developed based on the classical CTM and fundamental diagram of mixed traffic flow. Finally, two simulation methods, mixed traffic flow CTM and micro-simulation, are designed to verify the effectiveness of the proposed model. Moreover, taking the moving bottleneck on the expressway as an example, the congestion characteristics of mixed traffic flow are analyzed using multiple indexes, such as average travel speed, congestion delay, and congestion scale. The results show the following: (i) CAVs can significantly alleviate traffic congestion, (ii) the duration of the bottleneck is positively correlated with the degree of traffic congestion, and (iii) The traffic congestion assessment results under different model parameters slightly differ, but the impact is negligible.