********************************************************************************
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/meme26 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus 

model:  mod=         zoops    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=      169    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 GGGTGKGGYNGG MEME-1	width =  12  sites =  71  llr = 600  p-value = 9.2e-004  E-value = 9.2e-004
********************************************************************************
--------------------------------------------------------------------------------
	Motif GGGTGKGGYNGG MEME-1 Description
--------------------------------------------------------------------------------
Simplified        A  :::2:111:321
pos.-specific     C  :::1:::16311
probability       G  a9a:a4991256
matrix            T  :1:7:5::3222

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

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

--------------------------------------------------------------------------------
	Motif GGGTGKGGYNGG MEME-1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 8.11396 E= 9.2e-004 
  -414  -1279    193   -314 
 -1279  -1279    189   -182 
  -314  -1279    195  -1279 
   -33   -184   -316    150 
 -1279  -1279    199  -1279 
  -156   -416     54    111 
  -182   -316    180   -314 
  -214   -184    177   -414 
  -314    120   -184     38 
    25     23    -16    -44 
   -23   -135    105    -56 
   -82    -99    116    -56 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif GGGTGKGGYNGG MEME-1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 12 nsites= 71 E= 9.2e-004 
 0.014085  0.000000  0.957746  0.028169 
 0.000000  0.000000  0.929577  0.070423 
 0.028169  0.000000  0.971831  0.000000 
 0.197183  0.070423  0.028169  0.704225 
 0.000000  0.000000  1.000000  0.000000 
 0.084507  0.014085  0.366197  0.535211 
 0.070423  0.028169  0.873239  0.028169 
 0.056338  0.070423  0.859155  0.014085 
 0.028169  0.577465  0.070423  0.323944 
 0.295775  0.295775  0.225352  0.183099 
 0.211268  0.098592  0.521127  0.169014 
 0.140845  0.126761  0.563380  0.169014 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif GGGTGKGGYNGG MEME-1 regular expression
--------------------------------------------------------------------------------
GGGTG[TG]GG[CT][ACG][GA]G
--------------------------------------------------------------------------------




Time  0.44 secs.

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


********************************************************************************
MOTIF AGRAGRCARRSC MEME-2	width =  12  sites =  18  llr = 183  p-value = 7.4e-002  E-value = 7.4e-002
********************************************************************************
--------------------------------------------------------------------------------
	Motif AGRAGRCARRSC MEME-2 Description
--------------------------------------------------------------------------------
Simplified        A  a35924:a35:1
pos.-specific     C  ::1::2a:2:48
probability       G  :74184::556:
matrix            T  :::1:::::::2

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

Multilevel           AGAAGGCAGAGC
consensus             AG AA  AGC 
sequence                         
                                 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif AGRAGRCARRSC MEME-2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 8.42162 E= 7.4e-002 
   201  -1081  -1081  -1081 
    16  -1081    152  -1081 
   101   -218     82  -1081 
   184  -1081   -218   -216 
   -16  -1081    163  -1081 
    65    -59     82  -1081 
 -1081    199  -1081  -1081 
   201  -1081  -1081  -1081 
    42    -59     99  -1081 
   101  -1081     99  -1081 
 -1081     82    114  -1081 
  -216    163  -1081    -58 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif AGRAGRCARRSC MEME-2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 7.4e-002 
 1.000000  0.000000  0.000000  0.000000 
 0.277778  0.000000  0.722222  0.000000 
 0.500000  0.055556  0.444444  0.000000 
 0.888889  0.000000  0.055556  0.055556 
 0.222222  0.000000  0.777778  0.000000 
 0.388889  0.166667  0.444444  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.333333  0.166667  0.500000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  0.444444  0.555556  0.000000 
 0.055556  0.777778  0.000000  0.166667 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif AGRAGRCARRSC MEME-2 regular expression
--------------------------------------------------------------------------------
A[GA][AG]A[GA][GA]CA[GA][AG][GC]C
--------------------------------------------------------------------------------




Time  0.82 secs.

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

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

CPU: Timothys-iMac.local

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