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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/meme47 -mod oops -dna -revcomp -brief 0 -nmotifs 2 -objfun nz -w 12 -hsfrac 0.5 -shuf 2 -nostatus 

model:  mod=          oops    nmotifs=         2    evt=           inf
objective function:           em=       Noise-injected 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=        0.5
        searchsize=  16900    norand=         no    csites=         -1
Letter frequencies in dataset:
A 0.249 C 0.251 G 0.251 T 0.249 
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 NMWGGGTGKGGY MEME-1	width =  12  sites = 169  llr = 895  p-value = 3.3e-003  E-value = 3.3e-003
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	Motif NMWGGGTGKGGY MEME-1 Description
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Simplified        A  225:1:211211
pos.-specific     C  24:::12:::25
probability       G  32:988183661
matrix            T  215:1:516213

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

Multilevel           GCTGGGTGTGGC
consensus            TAA   C G  T
sequence             A           
                                 
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	Motif NMWGGGTGKGGY MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 19507 bayes= 6.24988 E= 3.3e-003 
   -11    -46     47     -7 
     0     76    -41    -87 
    89   -440   -241     95 
  -281   -440    187   -281 
  -178   -370    171   -156 
  -254   -148    173   -300 
   -61    -18   -176    112 
  -178   -255    166   -146 
  -113   -423     33    117 
   -72   -295    137    -56 
   -81    -65    121   -107 
  -139     98   -141     34 
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	Motif NMWGGGTGKGGY MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 169 E= 3.3e-003 
 0.230696  0.183506  0.349186  0.236613 
 0.248447  0.426109  0.189423  0.136021 
 0.461465  0.011908  0.047411  0.479216 
 0.035429  0.011908  0.917233  0.035429 
 0.072402  0.019314  0.824047  0.084237 
 0.042816  0.090320  0.835882  0.030982 
 0.162667  0.221949  0.074020  0.541365 
 0.072439  0.042945  0.794425  0.090191 
 0.113859  0.013360  0.315135  0.557646 
 0.150832  0.032600  0.647984  0.168584 
 0.141938  0.159837  0.579955  0.118269 
 0.094601  0.497115  0.094748  0.313536 
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	Motif NMWGGGTGKGGY MEME-1 regular expression
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[GTA][CA][TA]GGG[TC]G[TG]GG[CT]
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Time  1.17 secs.

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MOTIF RCWGAGCAGAGA MEME-2	width =  12  sites = 169  llr = 716  p-value = 3.6e-001  E-value = 3.6e-001
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	Motif RCWGAGCAGAGA MEME-2 Description
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Simplified        A  525252281727
pos.-specific     C  1511116:1:21
probability       G  3216352:7151
matrix            T  113111:1:121

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

Multilevel           ACAGAGCAGAGA
consensus            G TAG A   C 
sequence                         
                                 
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	Motif RCWGAGCAGAGA MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 19507 bayes= 6.24988 E= 3.6e-001 
   108   -171     21   -122 
   -43    104    -40   -120 
   107   -195   -150     39 
   -31    -95    118   -131 
   110   -195      5    -81 
   -39    -89    111    -93 
   -17    122    -69   -275 
   177   -381   -381   -107 
   -93   -124    153   -281 
   157   -282    -76   -169 
   -44    -32     88    -69 
   148   -143    -90   -161 
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	Motif RCWGAGCAGAGA MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 169 E= 3.6e-001 
 0.526517  0.077034  0.290051  0.106398 
 0.184791  0.516392  0.190948  0.107868 
 0.520599  0.065199  0.088868  0.325333 
 0.201073  0.130288  0.568158  0.100481 
 0.532434  0.065199  0.260466  0.141901 
 0.189239  0.136205  0.544489  0.130067 
 0.220294  0.587398  0.155445  0.036862 
 0.846043  0.017862  0.017862  0.118233 
 0.130067  0.106619  0.727921  0.035392 
 0.739534  0.035614  0.148040  0.076813 
 0.183321  0.201294  0.461649  0.153736 
 0.690727  0.093297  0.134717  0.081260 
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	Motif RCWGAGCAGAGA MEME-2 regular expression
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[AG]C[AT][GA][AG]G[CA]AGA[GC]A
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Time  2.18 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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