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This work applies Large Eddy Simulation (LES) to the combustion process within a CAI engine. The chemical reaction is treated with a pre-tabulation approach based on homogeneous reactor simulations. At this juncture, a five-dimensional chemistry database is employed where the thermo-chemical properties are a function of the unburnt gas temperature, the air–fuel ratio, the exhaust gas ratio, the pressure, and the reaction progress variable. Statistical quantities are gathered for 20 simulated cycles and the averaged pressure curves get compared to measurements. The simulation data are then used to provide further insight into the auto-ignition process. It will be shown how thermo-chemical states are distributed within the cylinder and how the ignition quality depends on them. A statistical analysis is conducted to identify manifolds in the multi-dimensional scalar space along which the conditions leading to ignition evolve. Furthermore the strong influence in between consecutive cycles caused by the exhaust gas is investigated to identify the mechanism of cycle-to-cycle variations.