See the file test_MarkovModel.py for an example of expected input:
>>> from Bio import MarkovModel
>>> states = ["0", "1", "2", "3"]
>>> alphabet = ["A", "C", "G", "T"]
>>> training_data = [
("AACCCGGGTTTTTTT", "001112223333333"),
("ACCGTTTTTTT", "01123333333"),
("ACGGGTTTTTT", "01222333333"),
("ACCGTTTTTTTT", "011233333333"),
]
>>> markov_model = MarkovModel.train_visible(states, alphabet, training_data)
>>> states = MarkovModel.find_states(markov_model, "AACGTT")
>>> print(states)
[(['0', '0', '1', '2', '3', '3'], 0.008212890625000005)]
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