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. 2018 Dec 13;14(12):e1006498. doi: 10.1371/journal.pcbi.1006498

Fig 3. Hidden Markov model used for trimming poly-A and poly-T heads and tails.

Fig 3

A head and tail states have a small (p = 0.01) probability to emit non-A bases, and similarly for T. The body state emits all four bases with equal probability. The start, and stop states emit nothing.