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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.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/meme38 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun cd -maxw 30 -searchsize 40000 -norand -nostatus 

model:  mod=         zoops    nmotifs=         2    evt=           inf
objective function:           em=       Central Enrichment: p-value of mean distance
                              starts=   Mean distance of best site from center
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=        yes    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 GCCACACCCWKCYNNBH MEME-1	width =  17  sites = 148  llr = 1308  p-value = 5.1e-004  E-value = 5.1e-004
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	Motif GCCACACCCWKCYNNBH MEME-1 Description
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Simplified        A  32:8:7:1:51222213
pos.-specific     C  1692a:a9a11533443
probability       G  61:::2::::4112221
matrix            T  ::1::1:::43253234

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

Multilevel           GCCACACCCAGCTTCCT
consensus            A    G   TT CCATC
sequence                          GTGA
                                  AG  
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	Motif GCCACACCCWKCYNNBH MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 17 n= 68385 bayes= 9.4654 E= 5.1e-004 
     5   -117    125   -241 
   -41    136    -88   -241 
  -241    185  -1302   -183 
   161    -34   -433   -441 
  -441    198   -433   -441 
   142   -433    -17   -160 
  -441    202  -1302  -1302 
  -183    187   -433   -341 
  -341    197  -1302   -341 
    99   -170   -636     69 
  -105    -72     67     41 
   -68    110    -98    -39 
   -68     14   -148     92 
   -28     15     -5     14 
   -20     54    -21    -28 
  -128     78    -19      3 
    -3     10   -159     67 
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	Motif GCCACACCCWKCYNNBH MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 17 nsites= 148 E= 5.1e-004 
 0.265060  0.108434  0.578313  0.048193 
 0.192771  0.626506  0.132530  0.048193 
 0.048193  0.879518  0.000000  0.072289 
 0.783133  0.192771  0.012048  0.012048 
 0.012048  0.963855  0.012048  0.012048 
 0.686747  0.012048  0.216867  0.084337 
 0.012048  0.987952  0.000000  0.000000 
 0.072289  0.891566  0.012048  0.024096 
 0.024096  0.951807  0.000000  0.024096 
 0.509112  0.075225  0.002936  0.412726 
 0.123570  0.147515  0.388478  0.340437 
 0.159714  0.521009  0.123418  0.195859 
 0.159714  0.267997  0.087274  0.485016 
 0.210995  0.270933  0.234788  0.283284 
 0.223043  0.355270  0.210692  0.210995 
 0.105649  0.418447  0.213628  0.262276 
 0.250227  0.261821  0.081098  0.406854 
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	Motif GCCACACCCWKCYNNBH MEME-1 regular expression
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[GA]CCAC[AG]CCC[AT][GT]C[TC][TCGA][CATG][CTG][TCA]
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Time  7.72 secs.

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MOTIF SAAWCCMCAYY MEME-2	width =  11  sites =  40  llr = 350  p-value = 2.9e-001  E-value = 3.4e-001
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	Motif SAAWCCMCAYY MEME-2 Description
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Simplified        A  :a94::5:a11
pos.-specific     C  6:129a5a:34
probability       G  4::::::::11
matrix            T  :::5:::::64

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

Multilevel           CAATCCACATC
consensus            G  A  C  CT
sequence                        
                                
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	Motif SAAWCCMCAYY MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 11 n= 69585 bayes= 11.9323 E= 3.4e-001 
  -463    122     75   -463 
   192   -463   -463   -463 
   173   -144   -229   -463 
    53    -52   -463     81 
  -268    192  -1129   -268 
  -268    198  -1129  -1129 
    90     98  -1129   -268 
 -1129    198   -260  -1129 
   190   -260  -1129  -1129 
  -235     25   -144    115 
  -150     75    -91     53 
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	Motif SAAWCCMCAYY MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 11 nsites= 40 E= 3.4e-001 
 0.010252  0.569748  0.409748  0.010252 
 0.970252  0.009748  0.009748  0.010252 
 0.850252  0.089748  0.049748  0.010252 
 0.370252  0.169748  0.009748  0.450252 
 0.040000  0.920000  0.000000  0.040000 
 0.040000  0.960000  0.000000  0.000000 
 0.480000  0.480000  0.000000  0.040000 
 0.000000  0.960000  0.040000  0.000000 
 0.960000  0.040000  0.000000  0.000000 
 0.050252  0.289748  0.089748  0.570252 
 0.090252  0.409748  0.129748  0.370252 
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	Motif SAAWCCMCAYY MEME-2 regular expression
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[CG]AA[TA]CC[AC]CA[TC][CT]
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Time 16.25 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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