********************************************************************************
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= Primary sequences shuffled preserving 2-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 common/Klf1-200-100.fa -oc results/meme34 -mod oops -dna -revcomp -brief 0 -nmotifs 2 -objfun se -w 12 -hsfrac 0.6 -shuf 2 -nostatus -mpi 

model:  mod=          oops    nmotifs=         2    evt=           inf
objective function:           em=       Selective mHG
                              starts=   log likelihood ratio (LLR)
strands: + -
width:  minw=           12    maxw=           12
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
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 TSTGTCTGYYMY MEME-1	width =  12  sites = 169  llr = 808  p-value = 4.7e-003  E-value = 4.7e-003
********************************************************************************
--------------------------------------------------------------------------------
	Motif TSTGTCTGYYMY MEME-1 Description
--------------------------------------------------------------------------------
Simplified        A  2:11:11:1131
pos.-specific     C  15:227:23455
probability       G  23:621:6211:
matrix            T  519261915413

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

Multilevel           TCTGTCTGTTCC
consensus             G  C  CCCAT
sequence                         
                                 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TSTGTCTGYYMY MEME-1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 6.25409 E= 4.7e-003 
   -46   -120    -58    112 
  -287    111     26   -102 
  -184   -350   -288    181 
  -197    -72    124    -40 
  -423    -27    -54    128 
  -187    157   -128   -164 
  -118   -360   -481    179 
  -264    -10    129   -116 
  -231     16    -48     97 
  -178     55    -87     76 
    36     89   -174    -82 
   -76     91   -265     46 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TSTGTCTGYYMY MEME-1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 12 nsites= 169 E= 4.7e-003 
 0.180418  0.109523  0.168694  0.541365 
 0.033959  0.542964  0.300360  0.122717 
 0.069462  0.022254  0.034088  0.874196 
 0.063545  0.152431  0.596218  0.187805 
 0.013268  0.208626  0.173123  0.604984 
 0.067992  0.748576  0.103606  0.079826 
 0.109412  0.020765  0.008931  0.860891 
 0.039876  0.235272  0.613970  0.110882 
 0.050241  0.281120  0.180529  0.488110 
 0.072439  0.368389  0.137620  0.421552 
 0.317983  0.466041  0.075508  0.140468 
 0.146385  0.471958  0.040005  0.341651 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TSTGTCTGYYMY MEME-1 regular expression
--------------------------------------------------------------------------------
T[CG]TG[TC]CT[GC][TC][TC][CA][CT]
--------------------------------------------------------------------------------




Time  0.33 secs.

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


********************************************************************************
MOTIF CCASCYYYTYCH MEME-2	width =  12  sites = 169  llr = 664  p-value = 7.0e-001  E-value = 7.0e-001
********************************************************************************
--------------------------------------------------------------------------------
	Motif CCASCYYYTYCH MEME-2 Description
--------------------------------------------------------------------------------
Simplified        A  117111111113
pos.-specific     C  781474542562
probability       G  1::41:111211
matrix            T  112115346324

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

Multilevel           CCAGCTCCTCCT
consensus              TC CTTCTTA
sequence                        C
                                 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif CCASCYYYTYCH MEME-2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 6.25409 E= 7.0e-001 
  -164    154   -216    -90 
  -124    165   -350   -161 
   144   -198   -316     -8 
  -193     59     72    -81 
   -93    145   -171   -122 
   -79     53   -276     88 
  -113    104   -148     17 
   -79     68   -148     54 
  -120    -19   -122    118 
  -178     90    -35      8 
  -159    132   -208    -11 
    36    -17   -228     71 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif CCASCYYYTYCH MEME-2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 12 nsites= 169 E= 7.0e-001 
 0.079790  0.730861  0.056305  0.133044 
 0.104928  0.791521  0.022291  0.081260 
 0.672976  0.063711  0.028208  0.235106 
 0.064978  0.378809  0.414312  0.141901 
 0.130067  0.686501  0.077034  0.106398 
 0.143371  0.362546  0.037102  0.456981 
 0.113786  0.516392  0.090356  0.279466 
 0.143371  0.403966  0.090356  0.362306 
 0.107868  0.220534  0.108108  0.563490 
 0.072365  0.469055  0.196865  0.261715 
 0.082730  0.627330  0.059282  0.230659 
 0.317946  0.223474  0.051877  0.406703 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif CCASCYYYTYCH MEME-2 regular expression
--------------------------------------------------------------------------------
CC[AT][GC]C[TC][CT][CT][TC][CT][CT][TAC]
--------------------------------------------------------------------------------




Time  0.61 secs.

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

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

CPU: Timothys-Mac-Mini.local

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