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Hercules profile HMM in full. Here we show the overall look at the complete graph that might be produced for a long read M where its tth character is Mt and Mt ∈ {A, T, G, C} 1 ≤ t ≤ n and n is the length of the long read M (i.e. |M| = n). In this example, there are n many match states and two insertion states for each match state. Only one character deletion is allowed at one transition because transitions may only skip one match state.
