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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= --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 -csites 30 common/Klf1-200-100.fa -oc results/meme9 -mod anr -dna -revcomp -brief 0 -nmotifs 2 -objfun classic -minw 8 -nostatus -mpi 

model:  mod=           anr    nmotifs=         2    evt=           inf
objective function:           em=       E-value of product of p-values
                              starts=   E-value of product of p-values
strands: + -
width:  minw=            8    maxw=           50
nsites: minsites=        2    maxsites=       30    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=           16900    N=             169
sample: seed=            0    hsfrac=          0
        searchsize=  16900    norand=         no    csites=         30
Letter frequencies in dataset:
A 0.248 C 0.252 G 0.252 T 0.248 
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 RGCCACACCCW MEME-1	width =  11  sites =  30  llr = 350  E-value = 3.6e-026
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	Motif RGCCACACCCW MEME-1 Description
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Simplified        A  531:8:a:::5
pos.-specific     C  ::9a2a:aaa1
probability       G  47:::::::::
matrix            T  1:1:::::::4

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

Multilevel           AGCCACACCCA
consensus            GA        T
sequence                        
                                
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	Motif RGCCACACCCW MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 11 n= 13237 bayes= 10.4897 E= 3.6e-026 
   101   -291     54   -131 
    10  -1155    154  -1155 
  -190    178  -1155   -190 
 -1155    199  -1155  -1155 
   175    -59  -1155  -1155 
 -1155    199  -1155  -1155 
   201  -1155  -1155  -1155 
 -1155    199  -1155  -1155 
 -1155    199  -1155  -1155 
 -1155    199  -1155  -1155 
   101    -92  -1155     56 
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	Motif RGCCACACCCW MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 11 nsites= 30 E= 3.6e-026 
 0.500000  0.033333  0.366667  0.100000 
 0.266667  0.000000  0.733333  0.000000 
 0.066667  0.866667  0.000000  0.066667 
 0.000000  1.000000  0.000000  0.000000 
 0.833333  0.166667  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.500000  0.133333  0.000000  0.366667 
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	Motif RGCCACACCCW MEME-1 regular expression
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[AG][GA]CCACACCC[AT]
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Time  3.29 secs.

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MOTIF SCTCCCHHTCTCTCCCCT MEME-2	width =  18  sites =  27  llr = 302  E-value = 2.8e-001
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	Motif SCTCCCHHTCTCTCCCCT MEME-2 Description
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Simplified        A  1:::2:34:3:1::1:12
pos.-specific     C  49:868422738:86681
probability       G  3::11:111::1:1:1::
matrix            T  21a112337:7:a13217

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

Multilevel           CCTCCCCATCTCTCCCCT
consensus            G   A AT AC   TT  
sequence                   TC          
                                       
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	Motif SCTCCCHHTCTCTCCCCT MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 18 n= 12054 bayes= 10.749 E= 2.8e-001 
  -174     82     24    -42 
  -274    176  -1140   -116 
 -1140  -1140   -276    195 
  -274    163   -176   -116 
   -16    124   -118   -174 
 -1140    170  -1140    -42 
    25     56   -176      6 
    58    -18   -118     25 
 -1140    -44   -176    158 
     6    141   -276   -274 
 -1140      4  -1140    158 
  -174    170   -118  -1140 
 -1140   -276  -1140    195 
 -1140    163   -176    -75 
  -174    132  -1140     25 
  -274    132   -118    -16 
  -116    163  -1140   -116 
   -42    -76  -1140    142 
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	Motif SCTCCCHHTCTCTCCCCT MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 18 nsites= 27 E= 2.8e-001 
 0.074074  0.444444  0.296296  0.185185 
 0.037037  0.851852  0.000000  0.111111 
 0.000000  0.000000  0.037037  0.962963 
 0.037037  0.777778  0.074074  0.111111 
 0.222222  0.592593  0.111111  0.074074 
 0.000000  0.814815  0.000000  0.185185 
 0.296296  0.370370  0.074074  0.259259 
 0.370370  0.222222  0.111111  0.296296 
 0.000000  0.185185  0.074074  0.740741 
 0.259259  0.666667  0.037037  0.037037 
 0.000000  0.259259  0.000000  0.740741 
 0.074074  0.814815  0.111111  0.000000 
 0.000000  0.037037  0.000000  0.962963 
 0.000000  0.777778  0.074074  0.148148 
 0.074074  0.629630  0.000000  0.296296 
 0.037037  0.629630  0.111111  0.222222 
 0.111111  0.777778  0.000000  0.111111 
 0.185185  0.148148  0.000000  0.666667 
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	Motif SCTCCCHHTCTCTCCCCT MEME-2 regular expression
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[CG]CTC[CA]C[CAT][ATC]T[CA][TC]CTC[CT][CT]CT
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Time  6.54 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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