********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 5.5.5 (Release date: Thu Sep 14 08:48:04 2023 +1000)

For further information on how to interpret these results please access https://meme-suite.org/meme.
To get a copy of the MEME Suite software please access https://meme-suite.org.

********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
If you use this program in your research, please cite:

Timothy L. Bailey and Charles Elkan,
"Fitting a mixture model by expectation maximization to
discover motifs in biopolymers",
Proceedings of the Second International Conference on Intelligent Systems
for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
PRIMARY SEQUENCES= common/Klf1-200-100.fa
CONTROL SEQUENCES= Primary sequences shuffled preserving 3-mers
ALPHABET= ACGT

********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme -p 4 common/Klf1-200-100.fa -oc results/meme27 -mod anr -dna -revcomp -brief 0 -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus 

model:  mod=           anr    nmotifs=         2    evt=           inf
objective function:           em=       Differential Enrichment mHG
                              starts=   log likelihood ratio (LLR)
strands: + -
width:  minw=           12    maxw=           12
nsites: minsites=        2    maxsites=      845    wnsites=       0.8
theta:  spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=           16900    N=             169
sample: seed=            0    hsfrac=        0.6
        searchsize=  16900    norand=         no    csites=         -1
Letter frequencies in dataset:
A 0.248 C 0.252 G 0.252 T 0.248 
Background letter frequencies (from file dataset with add-one prior applied):
A 0.248 C 0.252 G 0.252 T 0.248 
Background model order: 0
********************************************************************************


********************************************************************************
MOTIF GGGTGKGGYMRG MEME-1	width =  12  sites =  50  llr = 435  p-value = 2.6e-002  E-value = 2.6e-002
********************************************************************************
--------------------------------------------------------------------------------
	Motif GGGTGKGGYMRG MEME-1 Description
--------------------------------------------------------------------------------
Simplified        A  1::3:111:43:
pos.-specific     C  ::11::::53:1
probability       G  8a9:a4892258
matrix            T  :::6:51:312:

         bits    2.0  *  *       
                 1.8  *  *       
                 1.6  *  *       
                 1.4  ** *  *    
Relative         1.2 *** * **   *
Entropy          1.0 *** * **   *
(12.6 bits)      0.8 *** * **   *
                 0.6 ***** **  **
                 0.4 ********* **
                 0.2 ************
                 0.0 ------------

Multilevel           GGGTGTGGCAGG
consensus               A G  TCA 
sequence                     G   
                                 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif GGGTGKGGYMRG MEME-1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 7.89158 E= 2.6e-002 
  -105  -1229    174   -263 
 -1229  -1229    199  -1229 
  -263   -207    184  -1229 
    17   -207   -265    132 
 -1229  -1229    199  -1229 
  -105   -365     60     95 
  -131  -1229    174   -205 
  -163   -265    181  -1229 
  -263     93    -33     17 
    53     43    -65    -83 
    27  -1229    110    -63 
  -263   -107    174  -1229 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif GGGTGKGGYMRG MEME-1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 12 nsites= 50 E= 2.6e-002 
 0.120000  0.000000  0.840000  0.040000 
 0.000000  0.000000  1.000000  0.000000 
 0.040000  0.060000  0.900000  0.000000 
 0.280000  0.060000  0.040000  0.620000 
 0.000000  0.000000  1.000000  0.000000 
 0.120000  0.020000  0.380000  0.480000 
 0.100000  0.000000  0.840000  0.060000 
 0.080000  0.040000  0.880000  0.000000 
 0.040000  0.480000  0.200000  0.280000 
 0.360000  0.340000  0.160000  0.140000 
 0.300000  0.000000  0.540000  0.160000 
 0.040000  0.120000  0.840000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif GGGTGKGGYMRG MEME-1 regular expression
--------------------------------------------------------------------------------
GGG[TA]G[TG]GG[CTG][AC][GA]G
--------------------------------------------------------------------------------




Time  0.62 secs.

********************************************************************************


********************************************************************************
MOTIF RSAGASAGACAS MEME-2	width =  12  sites =  20  llr = 187  p-value = 5.1e-001  E-value = 5.1e-001
********************************************************************************
--------------------------------------------------------------------------------
	Motif RSAGASAGACAS MEME-2 Description
--------------------------------------------------------------------------------
Simplified        A  4273a:a:a37:
pos.-specific     C  14:1:6:3:714
probability       G  65:614:8:1:6
matrix            T  ::31::::::3:

         bits    2.0       * *   
                 1.8     * * *   
                 1.6     * * *   
                 1.4     * * *   
Relative         1.2   * * ***   
Entropy          1.0   * *****  *
(13.5 bits)      0.8   * ********
                 0.6 ************
                 0.4 ************
                 0.2 ************
                 0.0 ------------

Multilevel           GGAGACAGACAG
consensus            ACTA G C ATC
sequence                         
                                 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif RSAGASAGACAS MEME-2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 10.1871 E= 5.1e-001 
    49   -133    113  -1097 
   -73     67     84  -1097 
   149  -1097  -1097     27 
     1   -133    125   -231 
   193  -1097   -233  -1097 
 -1097    125     67  -1097 
   201  -1097  -1097  -1097 
 -1097     -1    158  -1097 
   201  -1097  -1097  -1097 
    27    137   -233  -1097 
   139   -233  -1097     27 
 -1097     67    125  -1097 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif RSAGASAGACAS MEME-2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 12 nsites= 20 E= 5.1e-001 
 0.350000  0.100000  0.550000  0.000000 
 0.150000  0.400000  0.450000  0.000000 
 0.700000  0.000000  0.000000  0.300000 
 0.250000  0.100000  0.600000  0.050000 
 0.950000  0.000000  0.050000  0.000000 
 0.000000  0.600000  0.400000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.250000  0.750000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.300000  0.650000  0.050000  0.000000 
 0.650000  0.050000  0.000000  0.300000 
 0.000000  0.400000  0.600000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif RSAGASAGACAS MEME-2 regular expression
--------------------------------------------------------------------------------
[GA][GC][AT][GA]A[CG]A[GC]A[CA][AT][GC]
--------------------------------------------------------------------------------




Time  1.10 secs.

********************************************************************************

********************************************************************************
Stopped because requested number of motifs (2) found.
********************************************************************************

CPU: Timothys-iMac.local

********************************************************************************
