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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/Klf1-200-100.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 -p 4 common/Klf1-200-100.fa -oc results/meme49 -mod anr -dna -revcomp -brief 0 -nmotifs 2 -objfun nz -w 12 -hsfrac 0.5 -shuf 2 -nostatus 

model:  mod=           anr    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=      845    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 CRGCCMCACCCW MEME-1	width =  12  sites =  77  llr = 711  p-value = 3.4e-005  E-value = 3.4e-005
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	Motif CRGCCMCACCCW MEME-1 Description
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Simplified        A  253216:7:::5
pos.-specific     C  51:784a:aaa1
probability       G  227::::2::::
matrix            T  12:12::1:::4

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

Multilevel           CAGCCACACCCA
consensus            GGA  C     T
sequence              T          
                                 
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	Motif CRGCCMCACCCW MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 19507 bayes= 9.22092 E= 3.4e-005 
   -45     85    -19    -80 
    91   -169     -3    -26 
    13   -269    142   -425 
   -56    145   -269   -126 
  -226    161  -1291    -45 
   133     58  -1291  -1291 
 -1291    199  -1291  -1291 
   152  -1291    -47   -126 
 -1291    199  -1291  -1291 
  -425    197  -1291  -1291 
 -1291    199  -1291  -1291 
   106    -95  -1291     50 
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	Motif CRGCCMCACCCW MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 77 E= 3.4e-005 
 0.181818  0.454545  0.220779  0.142857 
 0.467532  0.077922  0.246753  0.207792 
 0.272727  0.038961  0.675325  0.012987 
 0.168831  0.688312  0.038961  0.103896 
 0.051948  0.766234  0.000000  0.181818 
 0.623377  0.376623  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.714286  0.000000  0.181818  0.103896 
 0.000000  1.000000  0.000000  0.000000 
 0.012987  0.987013  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.519481  0.129870  0.000000  0.350649 
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	Motif CRGCCMCACCCW MEME-1 regular expression
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[CG][AGT][GA]CC[AC]CACCC[AT]
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Time  3.17 secs.

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MOTIF AGRAKCTGAWAA MEME-2	width =  12  sites =  15  llr = 162  p-value = 8.0e-001  E-value = 1.5e+000
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	Motif AGRAKCTGAWAA MEME-2 Description
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Simplified        A  9:57::::65a7
pos.-specific     C  :::1:7::3:::
probability       G  :a5152:a:1:3
matrix            T  1::151a:14::

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

Multilevel           AGGAGCTGAAAA
consensus              A TG  CT G
sequence                         
                                 
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	Motif AGRAKCTGAWAA MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 19507 bayes= 11.0366 E= 1.5e+000 
   191  -1055  -1055   -190 
 -1055  -1055    199  -1055 
    91  -1055    108  -1055 
   142   -191    -91    -90 
 -1055  -1055    108     91 
 -1055    141    -33    -90 
 -1055  -1055  -1055    201 
 -1055  -1055    199  -1055 
   127      8  -1055    -90 
   110  -1055   -191     69 
   201  -1055  -1055  -1055 
   156  -1055      8  -1055 
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	Motif AGRAKCTGAWAA MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 15 E= 1.5e+000 
 0.933333  0.000000  0.000000  0.066667 
 0.000000  0.000000  1.000000  0.000000 
 0.466667  0.000000  0.533333  0.000000 
 0.666667  0.066667  0.133333  0.133333 
 0.000000  0.000000  0.533333  0.466667 
 0.000000  0.666667  0.200000  0.133333 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.600000  0.266667  0.000000  0.133333 
 0.533333  0.000000  0.066667  0.400000 
 1.000000  0.000000  0.000000  0.000000 
 0.733333  0.000000  0.266667  0.000000 
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	Motif AGRAKCTGAWAA MEME-2 regular expression
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AG[GA]A[GT][CG]TG[AC][AT]A[AG]
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Time  5.56 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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