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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/meme36 -mod anr -dna -revcomp -brief 0 -nmotifs 2 -objfun se -w 12 -hsfrac 0.6 -shuf 2 -nostatus -mpi 

model:  mod=           anr    nmotifs=         2    evt=           inf
objective function:           em=       Selective 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=        0.6
        searchsize=  16900    norand=         no    csites=         -1
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 GGTGTGGYCKGV MEME-1	width =  12  sites =  31  llr = 289  p-value = 3.5e-003  E-value = 3.5e-003
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	Motif GGTGTGGYCKGV MEME-1 Description
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Simplified        A  ::::2:::21:2
pos.-specific     C  :3::::255::4
probability       G  a7:a298124a4
matrix            T  ::a:61:415::

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

Multilevel           GGTGTGGCCTGC
consensus             C  A  TAG G
sequence                        A
                                 
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	Motif GGTGTGGYCKGV MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 9.25185 E= 3.5e-003 
 -1160  -1160    194   -294 
 -1160     21    150  -1160 
  -294  -1160  -1160    196 
 -1160   -296    194  -1160 
   -14  -1160    -38    122 
 -1160   -296    184   -194 
  -294    -64    168  -1160 
 -1160    112   -196     64 
   -14    112    -64   -194 
   -94  -1160     62     96 
 -1160  -1160    194   -294 
   -30     65     53   -262 
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	Motif GGTGTGGYCKGV MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 31 E= 3.5e-003 
 0.000000  0.000000  0.967742  0.032258 
 0.000000  0.290323  0.709677  0.000000 
 0.032258  0.000000  0.000000  0.967742 
 0.000000  0.032258  0.967742  0.000000 
 0.225806  0.000000  0.193548  0.580645 
 0.000000  0.032258  0.903226  0.064516 
 0.032258  0.161290  0.806452  0.000000 
 0.000000  0.548387  0.064516  0.387097 
 0.225806  0.548387  0.161290  0.064516 
 0.129032  0.000000  0.387097  0.483871 
 0.000000  0.000000  0.967742  0.032258 
 0.201563  0.395212  0.362953  0.040272 
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	Motif GGTGTGGYCKGV MEME-1 regular expression
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G[GC]TG[TA]GG[CT][CA][TG]G[CGA]
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Time  0.42 secs.

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MOTIF CCYTGYCYCTTC MEME-2	width =  12  sites =  18  llr = 173  p-value = 6.9e-001  E-value = 6.9e-001
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	Motif CCYTGYCYCTTC MEME-2 Description
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Simplified        A  :1:1:::::::2
pos.-specific     C  974:3376a:16
probability       G  1:::72::::31
matrix            T  :2691534:a72

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

Multilevel           CCTTGTCCCTTC
consensus              C CCTT  G 
sequence                         
                                 
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	Motif CCYTGYCYCTTC MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 8.19635 E= 6.9e-001 
 -1081    191   -218  -1081 
  -116    152  -1081    -58 
 -1081     63  -1081    130 
  -116  -1081  -1081    184 
 -1081     14    141   -216 
 -1081     41    -59    101 
 -1081    152  -1081     16 
 -1081    128  -1081     65 
 -1081    199  -1081  -1081 
 -1081  -1081  -1081    201 
 -1081   -218     14    142 
   -58    114   -118    -58 
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	Motif CCYTGYCYCTTC MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 6.9e-001 
 0.000000  0.944444  0.055556  0.000000 
 0.111111  0.722222  0.000000  0.166667 
 0.000000  0.388889  0.000000  0.611111 
 0.111111  0.000000  0.000000  0.888889 
 0.000000  0.277778  0.666667  0.055556 
 0.000000  0.333333  0.166667  0.500000 
 0.000000  0.722222  0.000000  0.277778 
 0.000000  0.611111  0.000000  0.388889 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.055556  0.277778  0.666667 
 0.166667  0.555556  0.111111  0.166667 
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	Motif CCYTGYCYCTTC MEME-2 regular expression
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CC[TC]T[GC][TC][CT][CT]CT[TG]C
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Time  0.79 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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