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MEME - Motif discovery tool
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MEME version 5.4.0 (Release date: Tue Mar 9 17:38:20 2021 -0800)

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 common/Klf1-200-100.fa -oc results/meme48 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun nz -w 12 -hsfrac 0.5 -shuf 2 -nostatus -mpi 

model:  mod=         zoops    nmotifs=         2    evt=           inf
objective function:           em=       Noise-injected mHG
                              starts=   log likelihood ratio (LLR)
strands: + -
width:  minw=           12    maxw=           12
nsites: minsites=        2    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 WGGGTGKGGCHB MEME-1	width =  12  sites =  60  llr = 591  p-value = 7.9e-005  E-value = 7.9e-005
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	Motif WGGGTGKGGCHB MEME-1 Description
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Simplified        A  4:::1::11:22
pos.-specific     C  ::::1::::732
probability       G  2aaa:a398:14
matrix            T  5:::8:7:1342

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

Multilevel           TGGGTGTGGCTG
consensus            A     G  TCC
sequence                       AT
                                 
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	Motif WGGGTGKGGCHB MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 19507 bayes= 8.43276 E= 7.9e-005 
    63  -1255    -75     91 
 -1255  -1255    199  -1255 
 -1255  -1255    199  -1255 
 -1255  -1255    199  -1255 
  -131    -92  -1255    163 
 -1255  -1255    199  -1255 
 -1255  -1255     41    142 
  -131  -1255    178   -290 
  -190   -291    164   -109 
 -1255    144  -1255     35 
   -20      8   -159     80 
   -44    -22     67    -31 
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	Motif WGGGTGKGGCHB MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 60 E= 7.9e-005 
 0.383333  0.000000  0.150000  0.466667 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.100000  0.133333  0.000000  0.766667 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.333333  0.666667 
 0.100000  0.000000  0.866667  0.033333 
 0.066667  0.033333  0.783333  0.116667 
 0.000000  0.683333  0.000000  0.316667 
 0.216667  0.266667  0.083333  0.433333 
 0.183333  0.216667  0.400000  0.200000 
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	Motif WGGGTGKGGCHB MEME-1 regular expression
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[TA]GGGTG[TG]GG[CT][TCA][GCT]
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Time  0.81 secs.

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MOTIF YCYTATCTCTSM MEME-2	width =  12  sites =  79  llr = 552  p-value = 1.9e-001  E-value = 2.1e-001
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	Motif YCYTATCTCTSM MEME-2 Description
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Simplified        A  13::6::::1:3
pos.-specific     C  56411:a17245
probability       G  ::::21::2:4:
matrix            T  316919:91722

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

Multilevel           CCTTATCTCTGC
consensus            TAC G   G CA
sequence                         
                                 
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	Motif YCYTATCTCTSM MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 19507 bayes= 8.29344 E= 2.1e-001 
  -125    109   -261     36 
    11    131   -261   -190 
  -429     69   -331    116 
  -429   -131   -331    179 
   126   -151    -14   -149 
  -329   -273   -173    179 
 -1295    194   -331   -429 
  -329   -173   -273    179 
  -329    144     -6   -229 
  -129    -61   -431    154 
  -329     55     73    -39 
    35     90   -331    -39 
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	Motif YCYTATCTCTSM MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 79 E= 2.1e-001 
 0.104411  0.534830  0.041159  0.319601 
 0.268968  0.623437  0.041159  0.066436 
 0.012658  0.405063  0.025316  0.556962 
 0.012658  0.101266  0.025316  0.860759 
 0.594937  0.088608  0.227848  0.088608 
 0.025316  0.037975  0.075949  0.860759 
 0.000000  0.962025  0.025316  0.012658 
 0.025316  0.075949  0.037975  0.860759 
 0.025316  0.683544  0.240506  0.050633 
 0.101266  0.164557  0.012658  0.721519 
 0.025316  0.367089  0.417722  0.189873 
 0.316456  0.468354  0.025316  0.189873 
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	Motif YCYTATCTCTSM MEME-2 regular expression
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[CT][CA][TC]T[AG]TCT[CG]T[GC][CA]
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Time  1.57 secs.

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Stopped because requested number of motifs (2) found.
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CPU: Timothys-Mac-Mini.local

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