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MEME - Motif discovery tool
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MEME version 5.5.3 (Release date: Sat Jun 10 16:19:38 2023 -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= 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 -p 4 -csites 30 common/Klf1-200-100.fa -oc results/meme8 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun classic -minw 8 -nostatus 

model:  mod=         zoops    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=      169    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 WCVCCSTGSACYTTGTTT MEME-1	width =  18  sites =   8  llr = 102  E-value = 2.4e+000
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	Motif WCVCCSTGSACYTTGTTT MEME-1 Description
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Simplified        A  4:4::1:1:61::::11:
pos.-specific     C  :83994:341653::331
probability       G  :331:4:6513:1:a:::
matrix            T  6:1:11a:11:56a:669

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

Multilevel           TCACCCTGGACCTTGTTT
consensus            AGC  G CC GTC  CC 
sequence               G               
                                       
--------------------------------------------------------------------------------

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	Motif WCVCCSTGSACYTTGTTT MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 18 n= 12054 bayes= 9.7075 E= 2.4e+000 
    59   -965   -965    133 
  -965    157     -1   -965 
    59     -1     -1    -99 
  -965    180   -101   -965 
  -965    180   -965    -99 
   -99     58     58    -99 
  -965   -965   -965    201 
   -99     -1    131   -965 
  -965     58     99    -99 
   133   -101   -101    -99 
   -99    131     -1   -965 
  -965     99   -965    101 
  -965     -1   -101    133 
  -965   -965   -965    201 
  -965   -965    199   -965 
   -99     -1   -965    133 
   -99     -1   -965    133 
  -965   -101   -965    182 
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	Motif WCVCCSTGSACYTTGTTT MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 18 nsites= 8 E= 2.4e+000 
 0.375000  0.000000  0.000000  0.625000 
 0.000000  0.750000  0.250000  0.000000 
 0.375000  0.250000  0.250000  0.125000 
 0.000000  0.875000  0.125000  0.000000 
 0.000000  0.875000  0.000000  0.125000 
 0.125000  0.375000  0.375000  0.125000 
 0.000000  0.000000  0.000000  1.000000 
 0.125000  0.250000  0.625000  0.000000 
 0.000000  0.375000  0.500000  0.125000 
 0.625000  0.125000  0.125000  0.125000 
 0.125000  0.625000  0.250000  0.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  0.250000  0.125000  0.625000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.125000  0.250000  0.000000  0.625000 
 0.125000  0.250000  0.000000  0.625000 
 0.000000  0.125000  0.000000  0.875000 
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	Motif WCVCCSTGSACYTTGTTT MEME-1 regular expression
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[TA][CG][ACG]CC[CG]T[GC][GC]A[CG][CT][TC]TG[TC][TC]T
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Time  1.16 secs.

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MOTIF CCAACCACCTYYCCC MEME-2	width =  15  sites =   4  llr = 66  E-value = 1.9e+004
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	Motif CCAACCACCTYYCCC MEME-2 Description
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Simplified        A  ::883:a::::::::
pos.-specific     C  88338a:aa:55aaa
probability       G  3::::::::::::::
matrix            T  :3:::::::a55:::

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

Multilevel           CCAACCACCTCCCCC
consensus            GTCCA     TT   
sequence                            
                                    
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	Motif CCAACCACCTYYCCC MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 15 n= 12561 bayes= 11.6162 E= 1.9e+004 
  -865    157     -1   -865 
  -865    157   -865      1 
   159     -1   -865   -865 
   159     -1   -865   -865 
     1    157   -865   -865 
  -865    199   -865   -865 
   201   -865   -865   -865 
  -865    199   -865   -865 
  -865    199   -865   -865 
  -865   -865   -865    201 
  -865     99   -865    101 
  -865     99   -865    101 
  -865    199   -865   -865 
  -865    199   -865   -865 
  -865    199   -865   -865 
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	Motif CCAACCACCTYYCCC MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 15 nsites= 4 E= 1.9e+004 
 0.000000  0.750000  0.250000  0.000000 
 0.000000  0.750000  0.000000  0.250000 
 0.750000  0.250000  0.000000  0.000000 
 0.750000  0.250000  0.000000  0.000000 
 0.250000  0.750000  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  0.000000  0.000000  1.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
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	Motif CCAACCACCTYYCCC MEME-2 regular expression
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[CG][CT][AC][AC][CA]CACCT[CT][CT]CCC
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Time  2.03 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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