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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/meme39 -mod oops -dna -revcomp -brief 0 -nmotifs 2 -objfun ce -maxw 30 -searchsize 40000 -nostatus 

model:  mod=          oops    nmotifs=         2    evt=           inf
objective function:           em=       Central Enrichment mBN
                              starts=   Central Enrichment binomial test
strands: + -
width:  minw=            8    maxw=           30
nsites: minsites=      200    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 WGGGTGTG MEME-1	width =   8  sites = 200  llr = 1337  p-value = 8.4e-001  E-value = 1.6e+000
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	Motif WGGGTGTG MEME-1 Description
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Simplified        A  3:::1:::
pos.-specific     C  ::::1:::
probability       G  1999:929
matrix            T  6:1:7:81

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

Multilevel           TGGGTGTG
consensus            A       
sequence                     
                             
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	Motif WGGGTGTG MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 70185 bayes= 9.49399 E= 1.6e+000 
    42   -384   -149    111 
  -327   -410    194   -327 
  -410   -410    190   -206 
  -236   -270    188   -410 
  -100   -139   -282    154 
  -245   -240    188   -442 
  -344   -442    -30    158 
  -344   -341    188   -213 
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	Motif WGGGTGTG MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 8 nsites= 200 E= 1.6e+000 
 0.343462  0.017003  0.086771  0.552764 
 0.026528  0.014169  0.932774  0.026528 
 0.014901  0.014169  0.909518  0.061412 
 0.049784  0.037425  0.897890  0.014901 
 0.128200  0.092731  0.034591  0.744479 
 0.046804  0.046219  0.895056  0.011920 
 0.023548  0.011335  0.197382  0.767734 
 0.023548  0.022963  0.895056  0.058432 
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	Motif WGGGTGTG MEME-1 regular expression
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[TA]GGGTGTG
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Time  4.30 secs.

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MOTIF RGRGARRG MEME-2	width =   8  sites = 200  llr = 1035  p-value = 9.8e-001  E-value = 3.0e+000
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	Motif RGRGARRG MEME-2 Description
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Simplified        A  51517441
pos.-specific     C  :1::::::
probability       G  49582568
matrix            T  ::::::::

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

Multilevel           AGGGAGGG
consensus            G A GAA 
sequence                     
                             
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	Motif RGRGARRG MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 70185 bayes= 9.58604 E= 3.0e+000 
   108   -348     70   -265 
  -183   -220    181   -380 
    86   -380    104   -380 
  -103   -380    178   -380 
   154   -422    -22   -302 
    68   -380    113   -282 
    57   -348    119   -265 
   -98   -348    176   -348 
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	Motif RGRGARRG MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 8 nsites= 200 E= 3.0e+000 
 0.540740  0.021760  0.396760  0.040740 
 0.071878  0.053122  0.856694  0.018306 
 0.464735  0.017408  0.499551  0.018306 
 0.125449  0.017408  0.838836  0.018306 
 0.745873  0.013056  0.209484  0.031587 
 0.411164  0.017408  0.535265  0.036164 
 0.380026  0.021760  0.557474  0.040740 
 0.130026  0.021760  0.825331  0.022883 
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	Motif RGRGARRG MEME-2 regular expression
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[AG]G[GA]G[AG][GA][GA]G
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Time  8.45 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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