The MEME Suite

Arid3a_primary A: 0.179645793597971 0.210100830864919 0.18297957170479 0.218158426414591 0.0870705802557497 0.0435293344848582 0.695645391274696 0.886231513936226 0.105526350481291 0.112302355076614 0.815030478488063 0.719906706101697 0.598597229834128 0.469818137392637 0.233954380973979 0.267838631058226 0.240559605564699 C: 0.266648735950844 0.218430924209102 0.213084153545938 0.203797703013696 0.110886816294852 0.0958703394836635 0.0104078225875119 0.00354104133931097 0.00470109424317215 0.181644431061179 0.045569847543415 0.0821358973477016 0.0458429114703258 0.282556547844063 0.229160661497462 0.231747372592299 0.300737862311012 G: 0.382823288901203 0.353259680323954 0.340965693699501 0.18760023292416 0.0821358973477016 0.045569847543415 0.181644431061179 0.00470109424317215 0.00354104133931097 0.0104078225875119 0.0958703394836635 0.110886816294852 0.0853202791343203 0.0573452956112842 0.190290024780233 0.133765504128307 0.201112183210201 T: 0.170882181549982 0.218208564602024 0.262970581049772 0.390443637647554 0.719906706101697 0.815030478488063 0.112302355076614 0.105526350481291 0.886231513936226 0.695645391274696 0.0435293344848582 0.0870705802557497 0.270239579561226 0.190280019152016 0.346594932748325 0.366648492221168 0.257590348914088 Arid5a_primary A: 0.177322769961677 0.160221841004699 0.852203018833067 0.961248539596473 0.0565398220443113 0.930330589214641 0.019950864688249 0.0411316382396864 0.233918811349109 0.339577406902739 0.285389335391289 0.572142692856743 0.285668980971376 0.342798848206545 C: 0.428313310855555 0.324571292259573 0.0267326703147277 0.00379831572782298 0.00400812936891674 0.0051379987521542 0.0141888286179256 0.0875059354874809 0.027935175632631 0.352987545623934 0.13471914100935 0.0784175907242025 0.184067740053308 0.230459946341397 G: 0.22903578216647 0.0324446387621822 0.073955464568744 0.0101183390736629 0.00787744708407332 0.00713820083753976 0.00678864795483705 0.0390246666857379 0.519604520580082 0.184315929397724 0.268289476918125 0.190434321213762 0.262198874546343 0.153946120466092 T: 0.165328137016298 0.482762227973546 0.0471088462834612 0.0248348056020407 0.931574601502699 0.057393211195665 0.959071658738988 0.832337759587095 0.218541492438178 0.123119118075603 0.311602046681237 0.159005395205293 0.268064404428973 0.272795084985967

Writes MEME motif format to standard output.

A probability matrix and optionally a log-odds matrix are output for each motif in the file. The probability matrix is computed using pseudo-counts consisting of the background frequency (see -bg, below) multiplied by the total pseudocounts (see -pseudo, below). The log-odds matrix uses the background frequencies in the denominator and is log base 2.

Option	Parameter	Description	Default Behaviour
General Options
-skip	ID	Skip the motif identified by ID. This option can be repeated to skip more than one motif.	Motifs are not skipped.
-numseqs	# seqs	Assume that the motif was created from # seqs sites.	Assume the motif was based on 20 sites.
-truncate_names		Truncate motif names at the first underscore in the UNIPROBE ID. If the UNIPROBE ID was "Arid3a_primary" then it would be shortened to just "Arid3a".	Keep the full UNIPROBE ID.
-numbers		Use a number based on the position in the input instead of the UNIPROBE ID as the motif identifier.	The UNIPROBE ID is used as the motif identifier.
-bg	background file	The background file should be a Markov background model. It contains the background frequencies of letters use for assigning pseudocounts. The background frequencies will be included in the resulting MEME file.	Uses uniform background frequencies.
-pseudo	total pseudocounts	Add total pseudocounts times letter background to each frequency.	No pseudocount is added.
-logodds		Include a log-odds matrix in the output. This is not required for versions of the MEME Suite ≥ 4.7.0.	The log-odds matrix is not included in the output.
-url	website	The provided website URL will be stored with the motif and this can be used by MEME Suite programs to provide a direct link to that information in their output. If website contains the keyword MOTIF_NAME the UNIPROBE ID is substituted in place of MOTIF_NAME in the output. For example if the url is http://big-box-of-motifs.com/motifs/MOTIF_NAME.html and the UNIPROBE ID is Arid3a_primary, the motif will contain a link to http://big-box-of-motifs.com/motifs/Arid3a_primary.html	The output does not include a URL with the motifs.
-sg	sg_file_name	File containing motif name and ID in 2 columns. The second column is substituted for MOTIF_NAME in the URL if -url is given.	The motif name is substituted for MOTIF_NAME.