def get_kmers(start,end,input_alignment):
    """
    Accepts as start and end position within a MSA and returns a dict of all of the kmers
    :param start: int
    :param end: int
    :param input_alignment: dict of sequences
    :return: dict of sequence kmers corresponding to the positions
    """
    kmers = {}
    seq_iter = input_alignment.keys()
    for seq_id in seq_iter :
        kmers[seq_id] = input_alignment[seq_id][start:end]
    return kmers