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MEME - Motif discovery tool
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MEME version 5.4.1 (Release date: Sat Aug 21 19:23:23 2021 -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= ./seqs-centered
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 ./seqs-centered -oc meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 15 -bfile ./background -dna -searchsize 100000 -time 2919 -revcomp -nostatus 

model:  mod=         zoops    nmotifs=         3    evt=           inf
objective function:           em=       E-value of product of p-values
                              starts=   E-value of product of p-values
strands: + -
width:  minw=            6    maxw=           15
nsites: minsites=        2    maxsites=    17848    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=         1784800    N=           17848
sample: seed=            0    hsfrac=          0
        searchsize= 100000    norand=         no    csites=       1000
Letter frequencies in dataset:
A 0.255 C 0.245 G 0.245 T 0.255 
Background letter frequencies (from file ./background):
A 0.258 C 0.242 G 0.242 T 0.258 
Background model order: 2
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MOTIF VTGACTCA MEME-1	width =   8  sites = 2355  llr = 21927  E-value = 4.6e-056
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	Motif VTGACTCA MEME-1 Description
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Simplified        A  4::a::2a
pos.-specific     C  3:::a:8:
probability       G  3:a:::::
matrix            T  :a:::a::

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

Multilevel           ATGACTCA
consensus            G     A 
sequence             C       
                             
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	Motif VTGACTCA MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 1659864 bayes= 11.7063 E= 4.6e-056 
    56     22     48  -1785 
 -1785  -1785  -1785    196 
 -1785  -1785    204   -824 
   196  -1785  -1785  -1785 
  -644    200   -332  -1785 
 -1785  -1785  -1785    196 
   -29    170  -1785  -1785 
   196  -1785  -1785  -1785 
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	Motif VTGACTCA MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 8 nsites= 2355 E= 4.6e-056 
 0.379193  0.282378  0.338429  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.999151  0.000849 
 1.000000  0.000000  0.000000  0.000000 
 0.002972  0.972824  0.024204  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.210616  0.789384  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
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	Motif VTGACTCA MEME-1 regular expression
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[AGC]TGACT[CA]A
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Time 458.48 secs.

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MOTIF CSSSSCCGCSSSSSS MEME-2	width =  15  sites = 930  llr = 8839  E-value = 1.2e-004
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	Motif CSSSSCCGCSSSSSS MEME-2 Description
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Simplified        A  ::::2::::::::::
pos.-specific     C  a56437827445554
probability       G  :54553172354346
matrix            T  ::::::1:121121:

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

Multilevel           CGCGGCCGCCGCCCG
consensus             CGCCG C GCGGGC
sequence                      T     
                                    
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	Motif CSSSSCCGCSSSSSS MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 15 n= 1534928 bayes= 12.9858 E= 1.2e-004 
 -1650    200   -301  -1650 
 -1650     91    117  -1650 
 -1650    141     56  -1650 
 -1650     89    111   -320 
   -75     42    111  -1650 
 -1650    154     28  -1650 
 -1650    176   -134   -166 
  -382      2    160  -1650 
 -1650    163    -67   -140 
  -255     87     37    -37 
  -338     70    108   -186 
  -326    111     72   -235 
  -400    114     18    -56 
 -1650    115     57   -135 
 -1650     65    132   -420 
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	Motif CSSSSCCGCSSSSSS MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 15 nsites= 930 E= 1.2e-004 
 0.000000  0.969892  0.030108  0.000000 
 0.000000  0.454839  0.545161  0.000000 
 0.000000  0.641935  0.358065  0.000000 
 0.000000  0.448387  0.523656  0.027957 
 0.152688  0.323656  0.523656  0.000000 
 0.000000  0.705376  0.294624  0.000000 
 0.000000  0.822581  0.095699  0.081720 
 0.018280  0.245161  0.736559  0.000000 
 0.000000  0.749462  0.152688  0.097849 
 0.044086  0.441935  0.313978  0.200000 
 0.024731  0.392473  0.511828  0.070968 
 0.026882  0.522581  0.400000  0.050538 
 0.016129  0.535484  0.274194  0.174194 
 0.000000  0.538710  0.360215  0.101075 
 0.000000  0.379570  0.606452  0.013978 
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	Motif CSSSSCCGCSSSSSS MEME-2 regular expression
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C[GC][CG][GC][GC][CG]C[GC]C[CGT][GC][CG][CG][CG][GC]
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Time 843.83 secs.

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MOTIF CYYCBCCTCCC MEME-3	width =  11  sites = 2024  llr = 16670  E-value = 1.1e+000
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	Motif CYYCBCCTCCC MEME-3 Description
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Simplified        A  :1::1::2:::
pos.-specific     C  854a398:a97
probability       G  :12:21:2:11
matrix            T  234:4126::3

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

Multilevel           CCCCTCCTCCC
consensus             TT C T   T
sequence                 G      
                                
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	Motif CYYCBCCTCCC MEME-3 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 11 n= 1606320 bayes= 11.782 E= 1.1e+000 
 -1763    172   -283    -64 
  -211     93    -75     37 
 -1763     79    -55     69 
 -1763    204   -662   -603 
  -144     13     -9     68 
 -1763    186   -191   -223 
 -1763    169  -1763    -24 
   -47   -613    -28    125 
 -1763    204   -662  -1763 
 -1763    188   -118  -1763 
 -1763    146   -216     12 
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	Motif CYYCBCCTCCC MEME-3 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 11 nsites= 2024 E= 1.1e+000 
 0.000000  0.800889  0.034091  0.165020 
 0.059783  0.462451  0.143775  0.333992 
 0.000000  0.418972  0.165514  0.415514 
 0.000000  0.993577  0.002470  0.003953 
 0.094862  0.265316  0.227767  0.412055 
 0.000000  0.880435  0.064723  0.054842 
 0.000000  0.781621  0.000000  0.218379 
 0.185771  0.003458  0.199605  0.611166 
 0.000000  0.997530  0.002470  0.000000 
 0.000000  0.892787  0.107213  0.000000 
 0.000000  0.665514  0.054348  0.280138 
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	Motif CYYCBCCTCCC MEME-3 regular expression
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C[CT][CT]C[TCG]C[CT]TCC[CT]
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Time 1225.17 secs.

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Stopped because requested number of motifs (3) found.
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CPU: noble-meme.grid.gs.washington.edu

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