********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 5.5.9 (Release date: Fri Nov 21 15:33:51 2025 -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.

********************************************************************************


********************************************************************************
REFERENCE
********************************************************************************
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.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
PRIMARY SEQUENCES= sequences.fa
CONTROL SEQUENCES= --none--
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
seq1                     1.0000     27  seq2                     1.0000     23  
seq3                     1.0000     13  
********************************************************************************

********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme sequences.fa -dna -oc . -nostatus -time 14400 -mod anr -nmotifs 3 -minw 3 -maxw 50 -objfun classic -minsites 2 -revcomp -markov_order 0 

model:  mod=           anr    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=            3    maxw=           27
nsites: minsites=        2    maxsites=       15    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=              63    N=               3
sample: seed=            0    hsfrac=          0
        searchsize=     63    norand=         no    csites=       1000
Letter frequencies in dataset:
A 0.31 C 0.19 G 0.19 T 0.31 
Background letter frequencies (from file dataset with add-one prior applied):
A 0.309 C 0.191 G 0.191 T 0.309 
Background model order: 0
********************************************************************************


********************************************************************************
MOTIF MRKTTGGT MEME-1	width =   8  sites =   5  llr = 41  E-value = 1.2e+000
********************************************************************************
--------------------------------------------------------------------------------
	Motif MRKTTGGT MEME-1 Description
--------------------------------------------------------------------------------
Simplified        A  44::::::
pos.-specific     C  6::::2::
probability       G  :64::8a2
matrix            T  ::6aa::8

         bits    2.4       * 
                 2.2       * 
                 1.9       * 
                 1.7    **** 
Relative         1.4    **** 
Entropy          1.2 ** *****
(11.8 bits)      1.0 ********
                 0.7 ********
                 0.5 ********
                 0.2 ********
                 0.0 --------

Multilevel           CGTTTGGT
consensus            AAG  C G
sequence                     
                             
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif MRKTTGGT MEME-1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value              Site
-------------            ------  ----- ---------            --------
seq3                         -      5  1.94e-05          G CGTTTGGT TACC      
seq1                         +      2  1.94e-05          A CGTTTGGT TATTTTACCA
seq2                         -     12  1.48e-04       GTTA AAGTTGGT AACCGAAACG
seq1                         -     16  1.48e-04       GTTA AAGTTGGT AAAATAACCA
seq2                         +      2  2.80e-04          T CGTTTCGG TTACCAACTT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif MRKTTGGT MEME-1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
seq3                              1.9e-05  4_[-1]_1
seq1                              0.00015  1_[+1]_6_[-1]_4
seq2                              0.00015  1_[+1]_2_[-1]_4
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif MRKTTGGT MEME-1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF MRKTTGGT width=8 seqs=5
seq3                     (    5) CGTTTGGT  1 
seq1                     (    2) CGTTTGGT  1 
seq2                     (   12) AAGTTGGT  1 
seq1                     (   16) AAGTTGGT  1 
seq2                     (    2) CGTTTCGG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif MRKTTGGT MEME-1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 8 n= 42 bayes= 3.92161 E= 1.2e+000 
    37    165   -897   -897 
    37   -897    165   -897 
  -897   -897    107     95 
  -897   -897   -897    169 
  -897   -897   -897    169 
  -897      7    207   -897 
  -897   -897    239   -897 
  -897   -897      7    137 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif MRKTTGGT MEME-1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 1.2e+000 
 0.400000  0.600000  0.000000  0.000000 
 0.400000  0.000000  0.600000  0.000000 
 0.000000  0.000000  0.400000  0.600000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.200000  0.800000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.200000  0.800000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif MRKTTGGT MEME-1 regular expression
--------------------------------------------------------------------------------
[CA][GA][TG]TT[GC]G[TG]
--------------------------------------------------------------------------------




Time  0.20 secs.

********************************************************************************


********************************************************************************
MOTIF AAC MEME-2	width =   3  sites =   2  llr = 8  E-value = 6.5e+002
********************************************************************************
--------------------------------------------------------------------------------
	Motif AAC MEME-2 Description
--------------------------------------------------------------------------------
Simplified        A  aa:
pos.-specific     C  ::a
probability       G  :::
matrix            T  :::

         bits    2.4   *
                 2.2   *
                 1.9   *
                 1.7 ***
Relative         1.4 ***
Entropy          1.2 ***
(5.8 bits)       1.0 ***
                 0.7 ***
                 0.5 ***
                 0.2 ***
                 0.0 ---

Multilevel           AAC
consensus               
sequence                
                        
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif AAC MEME-2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value             Site  
-------------            ------  ----- ---------            ---
seq2                         +     21  1.83e-02 TACCAACTTT AAC           
seq1                         +     25  1.83e-02 TACCAACTTT AAC           
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif AAC MEME-2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
seq2                                0.018  20_[+2]
seq1                                0.018  24_[+2]
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif AAC MEME-2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF AAC width=3 seqs=2
seq2                     (   21) AAC  1 
seq1                     (   25) AAC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif AAC MEME-2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 3 n= 57 bayes= 4.78136 E= 6.5e+002 
   169   -765   -765   -765 
   169   -765   -765   -765 
  -765    239   -765   -765 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif AAC MEME-2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 3 nsites= 2 E= 6.5e+002 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif AAC MEME-2 regular expression
--------------------------------------------------------------------------------
AAC
--------------------------------------------------------------------------------




Time  0.38 secs.

********************************************************************************


********************************************************************************
MOTIF TWT MEME-3	width =   3  sites =   2  llr = 6  E-value = 3.2e+003
********************************************************************************
--------------------------------------------------------------------------------
	Motif TWT MEME-3 Description
--------------------------------------------------------------------------------
Simplified        A  :5:
pos.-specific     C  :::
probability       G  :::
matrix            T  a5a

         bits    2.4    
                 2.2    
                 1.9    
                 1.7 * *
Relative         1.4 * *
Entropy          1.2 * *
(4.1 bits)       1.0 * *
                 0.7 ***
                 0.5 ***
                 0.2 ***
                 0.0 ---

Multilevel           TAT
consensus             T 
sequence                
                        
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TWT MEME-3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value             Site  
-------------            ------  ----- ---------            ---
seq1                         +     13  5.96e-02 GTTTGGTTAT TTT ACCAACTTTA
seq1                         +     10  5.96e-02  ACGTTTGGT TAT TTTACCAACT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TWT MEME-3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
seq1                                 0.06  9_[+3]_[+3]_12
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TWT MEME-3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF TWT width=3 seqs=2
seq1                     (   13) TTT  1 
seq1                     (   10) TAT  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TWT MEME-3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 3 n= 57 bayes= 1.8467 E= 3.2e+003 
  -765   -765   -765    169 
    69   -765   -765     69 
  -765   -765   -765    169 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TWT MEME-3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 3 nsites= 2 E= 3.2e+003 
 0.000000  0.000000  0.000000  1.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TWT MEME-3 regular expression
--------------------------------------------------------------------------------
T[AT]T
--------------------------------------------------------------------------------




Time  0.55 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
seq1                             1.72e-02  1_[+1(1.94e-05)]_18
seq2                             5.98e-02  23
seq3                             3.36e-03  4_[-1(1.94e-05)]_1
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because requested number of motifs (3) found.
********************************************************************************

CPU: noble-meme.grid.gs.washington.edu

********************************************************************************
