delete_ambiguous: Marks sequences for deletion by replacing all
    chars with 'X'. These seqs are deleted later with remove_empty

def ambiguate(sequence1, sequence2, delete_ambiguous=False):
    """ delete_ambiguous: Marks sequences for deletion by replacing all
    chars with 'X'. These seqs are deleted later with remove_empty """
    delete = False
    combination = list()
    z = list(zip(sequence1, sequence2))
    for (a, b) in z:
        if a == b:
            combination.append(a)
        else:
            if a == '-' or b == '-':
                combination.append('-')
            else:
                if delete_ambiguous:
                    delete = True
                ambig = get_ambiguity(a, b)
                combination.append(ambig)
    if delete:
        return 'X' * len(combination)
    return ''.join(combination)