********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 5.4.0 (Release date: Tue Mar 9 17:38:20 2021 -0800)

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= --none--
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 -csites 30 common/Klf1-200-100.fa -oc results/meme7 -mod oops -dna -revcomp -brief 0 -nmotifs 2 -objfun classic -minw 8 -nostatus -mpi 

model:  mod=          oops    nmotifs=         2    evt=           inf
objective function:           em=       E-value of product of p-values
                              starts=   E-value of product of p-values
strands: + -
width:  minw=            8    maxw=           50
nsites: minsites=      169    maxsites=      169    wnsites=       0.8
theta:  spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
trim:   wg=             11    ws=              1    endgaps=       yes
data:   n=           16900    N=             169
sample: seed=            0    hsfrac=          0
        searchsize=  16900    norand=         no    csites=         30
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 VAGMRRCMAGR MEME-1	width =  11  sites = 169  llr = 772  E-value = 3.2e+013
********************************************************************************
--------------------------------------------------------------------------------
	Motif VAGMRRCMAGR MEME-1 Description
--------------------------------------------------------------------------------
Simplified        A  48154415925
pos.-specific     C  3:131:63:12
probability       G  3:72352:173
matrix            T  :21:2112:::

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

Multilevel           AAGAAGCAAGA
consensus            C  CGAGC  G
sequence             G         C
                                
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif VAGMRRCMAGR MEME-1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 11 n= 13237 bayes= 7.83298 E= 3.2e+013 
    56     29     15   -239 
   165   -340   -260    -69 
  -135   -112    155   -231 
   110     15    -54   -423 
    76   -150     42    -69 
    59   -260     98   -149 
  -141    130    -13   -211 
    87     42   -341    -44 
   182   -508   -192   -235 
   -52   -220    155   -275 
    95    -12     11   -381 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif VAGMRRCMAGR MEME-1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 11 nsites= 169 E= 3.2e+013 
 0.366790  0.307766  0.278180  0.047264 
 0.780991  0.023742  0.041494  0.153772 
 0.097578  0.115440  0.736742  0.050241 
 0.533978  0.279632  0.173123  0.013268 
 0.420081  0.088794  0.337315  0.153809 
 0.372744  0.041457  0.497078  0.088721 
 0.093168  0.619850  0.229318  0.057665 
 0.455584  0.337315  0.023705  0.183395 
 0.877173  0.007443  0.066614  0.048770 
 0.173031  0.054780  0.735253  0.036936 
 0.479253  0.230806  0.272226  0.017715 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif VAGMRRCMAGR MEME-1 regular expression
--------------------------------------------------------------------------------
[ACG]AG[AC][AG][GA][CG][AC]AG[AGC]
--------------------------------------------------------------------------------




Time  0.47 secs.

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


********************************************************************************
MOTIF MCACCCWG MEME-2	width =   8  sites = 169  llr = 757  E-value = 8.7e+023
********************************************************************************
--------------------------------------------------------------------------------
	Motif MCACCCWG MEME-2 Description
--------------------------------------------------------------------------------
Simplified        A  618:2162
pos.-specific     C  38:87911
probability       G  ::11:::5
matrix            T  1:111:42

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

Multilevel           ACACCCAG
consensus            C     T 
sequence                     
                             
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif MCACCCWG MEME-2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 8 n= 13744 bayes= 7.88744 E= 8.7e+023 
   123     39   -350   -197 
  -154    175   -323   -249 
   162   -271    -92   -200 
  -264    174   -212   -197 
   -71    142   -288    -82 
  -169    176   -282   -281 
   115   -208   -340     56 
   -39   -109    102    -44 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif MCACCCWG MEME-2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 8 nsites= 169 E= 8.7e+023 
 0.584255  0.329946  0.022254  0.063545 
 0.085707  0.843287  0.026719  0.044287 
 0.766180  0.038554  0.133228  0.062038 
 0.039839  0.838859  0.057794  0.063508 
 0.152266  0.673178  0.034125  0.140431 
 0.076813  0.852182  0.035614  0.035392 
 0.550185  0.059282  0.023779  0.366753 
 0.189239  0.118454  0.508986  0.183321 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif MCACCCWG MEME-2 regular expression
--------------------------------------------------------------------------------
[AC]CACCC[AT]G
--------------------------------------------------------------------------------




Time  0.86 secs.

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

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

CPU: Timothys-Mac-Mini.local

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