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MEME - Motif discovery tool
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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.

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REFERENCE
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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.
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TRAINING SET
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PRIMARY SEQUENCES= common/Klf1-200-100.fa
CONTROL SEQUENCES= Primary sequences shuffled preserving 2-mers
ALPHABET= ACGT

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COMMAND LINE SUMMARY
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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/meme35 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun se -w 12 -hsfrac 0.6 -shuf 2 -nostatus 

model:  mod=         zoops    nmotifs=         2    evt=           inf
objective function:           em=       Selective 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
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MOTIF CWGGGTGTGGYY MEME-1	width =  12  sites =  42  llr = 454  p-value = 3.0e-008  E-value = 3.0e-008
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	Motif CWGGGTGTGGYY MEME-1 Description
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Simplified        A  14:::::::1:2
pos.-specific     C  6::::1:::163
probability       G  1:aaa:a1a7:1
matrix            T  16:::8:9:134

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

Multilevel           CTGGGTGTGGCT
consensus             A        TC
sequence                         
                                 
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	Motif CWGGGTGTGGYY MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 8.30462 E= 3.0e-008 
   -80    118    -82    -80 
    70  -1204   -340    120 
 -1204  -1204    199  -1204 
 -1204  -1204    196   -338 
 -1204  -1204    199  -1204 
  -238   -108  -1204    175 
 -1204  -1204    199  -1204 
 -1204  -1204   -108    183 
 -1204  -1204    199  -1204 
  -180   -182    155   -106 
  -338    135  -1204     42 
   -58     41   -140     70 
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	Motif CWGGGTGTGGYY MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 42 E= 3.0e-008 
 0.142857  0.571429  0.142857  0.142857 
 0.404762  0.000000  0.023810  0.571429 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.976190  0.023810 
 0.000000  0.000000  1.000000  0.000000 
 0.047619  0.119048  0.000000  0.833333 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.119048  0.880952 
 0.000000  0.000000  1.000000  0.000000 
 0.071429  0.071429  0.738095  0.119048 
 0.023810  0.642857  0.000000  0.333333 
 0.166667  0.333333  0.095238  0.404762 
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	Motif CWGGGTGTGGYY MEME-1 regular expression
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C[TA]GGGTGTGG[CT][TC]
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Time  0.52 secs.

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MOTIF CTCCYTCTSCCY MEME-2	width =  12  sites =  33  llr = 273  p-value = 4.1e-001  E-value = 4.1e-001
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	Motif CTCCYTCTSCCY MEME-2 Description
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Simplified        A  12:2:2::::1:
pos.-specific     C  8:88628:4873
probability       G  1:2:::1:51::
matrix            T  17::461a1127

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

Multilevel           CTCCCTCTGCCT
consensus             AGAT   C TC
sequence                         
                                 
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	Motif CTCCYTCTSCCY MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 8.39895 E= 4.1e-001 
  -203    159   -205   -103 
    -4  -1169   -305    155 
 -1169    159    -25   -303 
   -23    159  -1169   -303 
  -303    127  -1169     55 
   -45    -47   -305    129 
  -303    165   -205   -103 
 -1169  -1169  -1169    201 
 -1169     75     85   -103 
 -1169    165   -147   -103 
  -203    147  -1169     -4 
 -1169     41  -1169    142 
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	Motif CTCCYTCTSCCY MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 33 E= 4.1e-001 
 0.060606  0.757576  0.060606  0.121212 
 0.242424  0.000000  0.030303  0.727273 
 0.000000  0.757576  0.212121  0.030303 
 0.212121  0.757576  0.000000  0.030303 
 0.030303  0.606061  0.000000  0.363636 
 0.181818  0.181818  0.030303  0.606061 
 0.030303  0.787879  0.060606  0.121212 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.424242  0.454545  0.121212 
 0.000000  0.787879  0.090909  0.121212 
 0.060606  0.696970  0.000000  0.242424 
 0.000000  0.333333  0.000000  0.666667 
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	Motif CTCCYTCTSCCY MEME-2 regular expression
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C[TA][CG][CA][CT]TCT[GC]C[CT][TC]
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Time  0.92 secs.

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Stopped because requested number of motifs (2) found.
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CPU: Timothys-iMac.local

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