meme inside_unassigned.fasta -o inside -protein

meme outside_unassigned.fasta -o outside -protein;

meme tm_unassigned.fasta -o tm -protein

meme all_unassigned.fasta -o unassigned -protein

    <dataset>               file containing sequences in FASTA format
    [-h]                    print this message
    [-o <output dir>]       name of directory for output files
                            will not replace existing directory
    [-oc <output dir>]      name of directory for output files
                            will replace existing directory
    [-text]                 output in text format (default is HTML)
    [-objfun classic|de|se|cd|ce]   objective function (default: classic)
    [-test mhg|mbn|mrs]     statistical test type (default: mhg)
    [-use_llr]              use LLR in search for starts in Classic mode
    [-neg <negdataset>]     file containing control sequences
    [-shuf <kmer>]          preserve frequencies of k-mers of size <kmer> 
                            when shuffling (default: 2)
    [-hsfrac <hsfrac>]      fraction of primary sequences in holdout set 
                            (default: 0.5)
    [-cefrac <cefrac>]      fraction sequence length for CE region 
                            (default: 0.25)
    [-searchsize <ssize>]   maximum portion of primary dataset to use
                            for motif search (in characters)
    [-maxsize <maxsize>]    maximum dataset size in characters
    [-norand]               do not randomize the order of the input 
                            sequences with -searchsize
    [-csites <csites>]      maximum number of sites for EM in Classic mode
    [-seed <seed>]          random seed for shuffling and sampling
    [-dna]                  sequences use DNA alphabet
    [-rna]                  sequences use RNA alphabet
    [-protein]              sequences use protein alphabet
    [-alph <alph file>]     sequences use custom alphabet
    [-revcomp]              allow sites on + or - DNA strands
    [-pal]                  force palindromes (requires -dna)
    [-mod oops|zoops|anr]   distribution of motifs
    [-nmotifs <nmotifs>]    maximum number of motifs to find
    [-evt <ev>]             stop if motif E-value greater than <evt>
    [-time <t>]             quit before <t> CPU seconds consumed
    [-nsites <sites>]       number of sites for each motif
    [-minsites <minsites>]  minimum number of sites for each motif
    [-maxsites <maxsites>]  maximum number of sites for each motif
    [-wnsites <wnsites>]    weight on expected number of sites
    [-w <w>]                motif width
    [-minw <minw>]          minimum motif width
    [-maxw <maxw>]          maximum motif width
    [-allw]                 test starts of all widths from minw to maxw
    [-nomatrim]             do not adjust motif width using multiple
                            alignment
    [-wg <wg>]              gap opening cost for multiple alignments
    [-ws <ws>]              gap extension cost for multiple alignments
    [-noendgaps]            do not count end gaps in multiple alignments
    [-bfile <bfile>]        name of background Markov model file
    [-markov_order <order>] (maximum) order of Markov model to use or create
    [-psp <pspfile>]        name of positional priors file
    [-maxiter <maxiter>]    maximum EM iterations to run
    [-distance <distance>]  EM convergence criterion
    [-prior dirichlet|dmix|mega|megap|addone]
                            type of prior to use
    [-b <b>]                strength of the prior
    [-plib <plib>]          name of Dirichlet prior file
    [-spfuzz <spfuzz>]      fuzziness of sequence to theta mapping
    [-spmap uni|pam]        starting point seq to theta mapping type
    [-cons <cons>]          consensus sequence to start EM from
    [-brief <n>]            omit sites and sequence tables in
                            output if more than <n> primary sequences
    [-nostatus]             do not print progress reports to terminal
    [-p <np>]               use parallel version with <np> processors
    [-sf <sf>]              print <sf> as name of sequence file
    [-V]                    verbose mode
    [-version]              display the version number and exit