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MEME - Motif discovery tool
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MEME version 5.5.3 (Release date: Sat Jun 10 16:19:38 2023 -0700)

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.fa
CONTROL SEQUENCES= --none--
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.fa -oc results/meme40 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun ce -maxw 30 -searchsize 40000 -nostatus 

model:  mod=         zoops    nmotifs=         2    evt=           inf
objective function:           em=       Central Enrichment mBN
                              starts=   Central Enrichment binomial test
strands: + -
width:  minw=            8    maxw=           30
nsites: minsites=        2    maxsites=      200    wnsites=       0.8
theta:  spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=          100000    N=             200
sample: seed=            0    hsfrac=        0.5
        searchsize=  40000    norand=         no    csites=         -1
Letter frequencies in dataset:
A 0.256 C 0.244 G 0.244 T 0.256 
Background letter frequencies (from file dataset with add-one prior applied):
A 0.256 C 0.244 G 0.244 T 0.256 
Background model order: 0
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MOTIF CTTATCTC MEME-1	width =   8  sites =  71  llr = 594  p-value = 5.4e-002  E-value = 5.5e-002
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	Motif CTTATCTC MEME-1 Description
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Simplified        A  1::a::2:
pos.-specific     C  91:::a:6
probability       G  :::::::2
matrix            T  :9a:a:71

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

Multilevel           CTTATCTC
consensus                  AG
sequence                     
                             
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	Motif CTTATCTC MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 70185 bayes= 11.639 E= 5.5e-002 
  -186    181   -317   -238 
  -356   -116  -1217    176 
 -1217  -1217  -1217    196 
   193  -1217   -348  -1217 
 -1217  -1217  -1217    196 
 -1217    204  -1217  -1217 
   -10   -348  -1217    153 
 -1217    137     -3    -97 
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	Motif CTTATCTC MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 8 nsites= 71 E= 5.5e-002 
 0.070789  0.853124  0.027037  0.049050 
 0.021739  0.108696  0.000000  0.869565 
 0.000000  0.000000  0.000000  1.000000 
 0.978261  0.000000  0.021739  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.239130  0.021739  0.000000  0.739130 
 0.000000  0.630435  0.239130  0.130435 
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	Motif CTTATCTC MEME-1 regular expression
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CTTATC[TA][CG]
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Time  5.73 secs.

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MOTIF GGGTGTGG MEME-2	width =   8  sites =  90  llr = 869  p-value = 2.7e-001  E-value = 3.2e-001
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	Motif GGGTGTGG MEME-2 Description
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Simplified        A  :::1::::
pos.-specific     C  :::1:::1
probability       G  aaa:a2a8
matrix            T  :::9:8:2

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

Multilevel           GGGTGTGG
consensus                    
sequence                     
                             
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	Motif GGGTGTGG MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 70185 bayes= 10.1527 E= 3.2e-001 
 -1234  -1234    204  -1234 
 -1234  -1234    204  -1234 
 -1234  -1234    204  -1234 
  -215   -208  -1234    179 
 -1234  -1234    204  -1234 
 -1234  -1234    -66    172 
 -1234  -1234    204  -1234 
 -1234   -208    166    -57 
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	Motif GGGTGTGG MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 8 nsites= 90 E= 3.2e-001 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.057692  0.057692  0.000000  0.884615 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.153846  0.846154 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.057692  0.769231  0.173077 
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	Motif GGGTGTGG MEME-2 regular expression
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GGGTGTGG
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Time 11.32 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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