def find_snp_positions(consensus):
    """
    Acccepts IUPAC masked pseudo consensus sequence and identifies the positions which are not A,T,C,G
    :param consensus: str sequence
    :return: list of variable positions
    """
    positions = []
    for i in range(0,len(consensus)):
        base = consensus[i]
        if base not in ['A','T','C','G','N','-']:
            positions.append(i)
    return positions