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MEME - Motif discovery tool
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MEME version 5.4.1 (Release date: Sat Aug 21 19:23:23 2021 -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= tutorial_short.fasta
CONTROL SEQUENCES= --none--
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
s1                       1.0000      6  s2                       1.0000      6  
s3                       1.0000      6  
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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 tutorial_short.fasta -w 3 -dna -nmotifs 3 

model:  mod=         zoops    nmotifs=         3    evt=           inf
objective function:           em=       E-value of product of p-values
                              starts=   E-value of product of p-values
strands: +
width:  minw=            3    maxw=            3
nsites: minsites=        2    maxsites=        3    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=              18    N=               3
sample: seed=            0    hsfrac=          0
        searchsize=     18    norand=         no    csites=       1000
Letter frequencies in dataset:
A 0.333 C 0.333 G 0.167 T 0.167 
Background letter frequencies (from file dataset with add-one prior applied):
A 0.318 C 0.318 G 0.182 T 0.182 
Background model order: 0
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MOTIF ACT MEME-1	width =   3  sites =   3  llr = 12  E-value = 2.5e-001
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	Motif ACT MEME-1 Description
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Simplified        A  a::
pos.-specific     C  :a:
probability       G  :::
matrix            T  ::a

         bits    2.5   *
                 2.2   *
                 2.0   *
                 1.7 ***
Relative         1.5 ***
Entropy          1.2 ***
(5.8 bits)       1.0 ***
                 0.7 ***
                 0.5 ***
                 0.2 ***
                 0.0 ---

Multilevel           ACT
consensus               
sequence                
                        
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	Motif ACT MEME-1 sites sorted by position p-value
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Sequence name             Start   P-value             Site  
-------------             ----- ---------            ---
s3                            4  1.84e-02        CGG ACT           
s2                            1  1.84e-02          . ACT CCA       
s1                            2  1.84e-02          A ACT GA        
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	Motif ACT MEME-1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
s3                                  0.018  3_[+1]
s2                                  0.018  [+1]_3
s1                                  0.018  1_[+1]_2
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	Motif ACT MEME-1 in BLOCKS format
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BL   MOTIF ACT width=3 seqs=3
s3                       (    4) ACT  1 
s2                       (    1) ACT  1 
s1                       (    2) ACT  1 
//

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	Motif ACT MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 3 n= 12 bayes= 2.15528 E= 2.5e-001 
   165   -823   -823   -823 
  -823    165   -823   -823 
  -823   -823   -823    246 
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	Motif ACT MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 3 nsites= 3 E= 2.5e-001 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
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	Motif ACT MEME-1 regular expression
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ACT
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Time  0.25 secs.

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MOTIF CSR MEME-2	width =   3  sites =   2  llr = 5  E-value = 3.5e+001
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	Motif CSR MEME-2 Description
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Simplified        A  ::5
pos.-specific     C  a5:
probability       G  :55
matrix            T  :::

         bits    2.5    
                 2.2    
                 2.0    
                 1.7 *  
Relative         1.5 *  
Entropy          1.2 *  
(3.8 bits)       1.0 ***
                 0.7 ***
                 0.5 ***
                 0.2 ***
                 0.0 ---

Multilevel           CCA
consensus             GG
sequence                
                        
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	Motif CSR MEME-2 sites sorted by position p-value
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Sequence name             Start   P-value             Site  
-------------             ----- ---------            ---
s3                            1  1.05e-02          . CGG ACT       
s2                            4  7.95e-02        ACT CCA           
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	Motif CSR MEME-2 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
s3                                  0.011  [+2]_3
s2                                   0.08  3_[+2]
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	Motif CSR MEME-2 in BLOCKS format
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BL   MOTIF CSR width=3 seqs=2
s3                       (    1) CGG  1 
s2                       (    4) CCA  1 
//

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	Motif CSR MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 3 n= 12 bayes= 2.32193 E= 3.5e+001 
  -765    165   -765   -765 
  -765     65    145   -765 
    65   -765    145   -765 
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	Motif CSR MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 3 nsites= 2 E= 3.5e+001 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
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	Motif CSR MEME-2 regular expression
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C[CG][AG]
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Time  0.42 secs.

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SUMMARY OF MOTIFS
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	Combined block diagrams: non-overlapping sites with p-value < 0.0001
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SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
s1                               1.42e-01  6
s2                               9.90e-02  6
s3                               2.03e-02  6
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Stopped because couldn't find any more starting points for EM.
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CPU: jiri-HP-Z2-Tower-G4-WS

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