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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/crp0.s
CONTROL SEQUENCES= --none--
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
ce1cg                    1.0000    105  ara                      1.0000    105  
bglr1                    1.0000    105  crp                      1.0000    105  
cya                      1.0000    105  deop2                    1.0000    105  
gale                     1.0000    105  ilv                      1.0000    105  
lac                      1.0000    105  male                     1.0000    105  
malk                     1.0000    105  malt                     1.0000    105  
ompa                     1.0000    105  tnaa                     1.0000    105  
uxu1                     1.0000    105  pbr322                   1.0000    105  
trn9cat                  1.0000    105  tdc                      1.0000    105  
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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 -minsites 3 -maxsites 17 common/crp0.s -oc results/meme3 -mod anr -dna -revcomp -nmotifs 2 -objfun classic -minw 8 -nostatus 

model:  mod=           anr    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=        3    maxsites=       17    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=            1890    N=              18
sample: seed=            0    hsfrac=          0
        searchsize=   1890    norand=         no    csites=       1000
Letter frequencies in dataset:
A 0.304 C 0.196 G 0.196 T 0.304 
Background letter frequencies (from file dataset with add-one prior applied):
A 0.304 C 0.196 G 0.196 T 0.304 
Background model order: 0
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MOTIF WWTAYKTGAWCNAYDTCACAM MEME-1	width =  21  sites =  17  llr = 195  E-value = 5.8e-004
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	Motif WWTAYKTGAWCNAYDTCACAM MEME-1 Description
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Simplified        A  45351::26412813:19:94
pos.-specific     C  1::2312:3272:3129:a:4
probability       G  :1:216:6:224223::1:1:
matrix            T  5472648112121438:1::2

         bits    2.4                   *  
                 2.1                   *  
                 1.9                 * *  
                 1.6                 * *  
Relative         1.4                 * ** 
Entropy          1.2       *        ***** 
(16.6 bits)      0.9   *  ***  * *  ***** 
                 0.7   *  **** * *  ***** 
                 0.5 *** ***** * *  ******
                 0.2 *** ***** **** ******
                 0.0 ---------------------

Multilevel           TATATGTGAACGATATCACAA
consensus            ATA CTCACT A CG     C
sequence                        C  T      
                                          
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	Motif WWTAYKTGAWCNAYDTCACAM MEME-1 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                    Site       
-------------            ------  ----- ---------            ---------------------
ara                          +     54  6.23e-09 GTCCACATTG ATTATTTGCACGGCGTCACAC TTTGCTATGC
ce1cg                        -     19  4.24e-07 CACCACGCGC TATTCTCGCCCGATGCCACAA AAACCAGCAC
pbr322                       -     55  5.29e-07 TCTCCTTACG CATCTGTGCGGTATTTCACAC CGCATATGGT
ompa                         +     47  8.08e-07 TTTTTTTTCA TATGCCTGACGGAGTTCACAC TTGTAAGTTT
malt                         -     43  8.96e-07 TTTATGTGTC TGAATTTGCACTGTGTCACAA TTCCAAATCT
crp                          +     62  8.96e-07 ATGTACTGCA TGTATGCAAAGGACGTCACAT TACCGTGCAG
uxu1                         -     19  1.33e-06 CCGAATTCTA ATTGGGTTAACCACATCACAA CAATTTCACT
deop2                        +      6  1.47e-06      AGTGA ATTATTTGAACCAGATCGCAT TACAGTGATG
ce1cg                        +     60  1.47e-06 TGAAAGACTG TTTTTTTGATCGTTTTCACAA AAATGGAAGT
lac                          -     75  1.77e-06 GTGAAATTGT TATCCGCTCACAATTCCACAC AACATACGAG
cya                          -     52  1.77e-06 AAAATGGTCT AAAACGTGATCAATTTAACAC CTTGCTGATT
male                         +     13  2.13e-06 ATTACCGCCA ATTCTGTAACAGAGATCACAC AAAGCGACGG
tnaa                         -     73  4.60e-06 TGAAATTGTT TAAATGTGAATCGAATCACAA TCGTTCGGGG
malk                         -     63  6.32e-06 ATCGCCACGA TTTTTGCAAGCAACATCACGA AATTCCTTAC
ilv                          +     38  6.82e-06 AATTCAGTAC AAAACGTGATCAACCCCTCAA TTTTCCCTTT
gale                         +     41  6.82e-06 AACGATTCCA CTAATTTATTCCATGTCACAC TTTTCGCATC
lac                          -     11  8.55e-06 TGGGGTGCCT AATGAGTGAGCTAACTCACAT TAATTGCGTT
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	Motif WWTAYKTGAWCNAYDTCACAM MEME-1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
ara                               6.2e-09  53_[+1]_31
ce1cg                             4.2e-07  18_[-1]_20_[+1]_25
pbr322                            5.3e-07  54_[-1]_30
ompa                              8.1e-07  46_[+1]_38
malt                                9e-07  42_[-1]_42
crp                                 9e-07  61_[+1]_23
uxu1                              1.3e-06  18_[-1]_66
deop2                             1.5e-06  5_[+1]_79
lac                               8.5e-06  10_[-1]_43_[-1]_10
cya                               1.8e-06  51_[-1]_33
male                              2.1e-06  12_[+1]_72
tnaa                              4.6e-06  72_[-1]_12
malk                              6.3e-06  62_[-1]_22
ilv                               6.8e-06  37_[+1]_47
gale                              6.8e-06  40_[+1]_44
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	Motif WWTAYKTGAWCNAYDTCACAM MEME-1 in BLOCKS format
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BL   MOTIF WWTAYKTGAWCNAYDTCACAM width=21 seqs=17
ara                      (   54) ATTATTTGCACGGCGTCACAC  1 
ce1cg                    (   19) TATTCTCGCCCGATGCCACAA  1 
pbr322                   (   55) CATCTGTGCGGTATTTCACAC  1 
ompa                     (   47) TATGCCTGACGGAGTTCACAC  1 
malt                     (   43) TGAATTTGCACTGTGTCACAA  1 
crp                      (   62) TGTATGCAAAGGACGTCACAT  1 
uxu1                     (   19) ATTGGGTTAACCACATCACAA  1 
deop2                    (    6) ATTATTTGAACCAGATCGCAT  1 
ce1cg                    (   60) TTTTTTTGATCGTTTTCACAA  1 
lac                      (   75) TATCCGCTCACAATTCCACAC  1 
cya                      (   52) AAAACGTGATCAATTTAACAC  1 
male                     (   13) ATTCTGTAACAGAGATCACAC  1 
tnaa                     (   73) TAAATGTGAATCGAATCACAA  1 
malk                     (   63) TTTTTGCAAGCAACATCACGA  1 
ilv                      (   38) AAAACGTGATCAACCCCTCAA  1 
gale                     (   41) CTAATTTATTCCATGTCACAC  1 
lac                      (   11) AATGAGTGAGCTAACTCACAT  1 
//

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	Motif WWTAYKTGAWCNAYDTCACAM MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 21 n= 1530 bayes= 6.47573 E= 5.8e-004 
    44    -73  -1073     63 
    63  -1073    -73     44 
    -5  -1073  -1073    121 
    63    -15    -15    -78 
  -237     59   -173     95 
 -1073   -173    159     21 
 -1073     26  -1073    133 
   -37  -1073    172   -137 
   109     59  -1073   -237 
    44    -15    -15    -37 
  -237    185    -15   -237 
   -37     26     85    -78 
   133  -1073    -15   -237 
  -137     59    -15     44 
    -5    -73     59     -5 
 -1073    -15  -1073    144 
  -237    226  -1073  -1073 
   154  -1073   -173   -237 
 -1073    235  -1073  -1073 
   163  -1073   -173  -1073 
    44    107  -1073    -78 
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	Motif WWTAYKTGAWCNAYDTCACAM MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 21 nsites= 17 E= 5.8e-004 
 0.411765  0.117647  0.000000  0.470588 
 0.470588  0.000000  0.117647  0.411765 
 0.294118  0.000000  0.000000  0.705882 
 0.470588  0.176471  0.176471  0.176471 
 0.058824  0.294118  0.058824  0.588235 
 0.000000  0.058824  0.588235  0.352941 
 0.000000  0.235294  0.000000  0.764706 
 0.235294  0.000000  0.647059  0.117647 
 0.647059  0.294118  0.000000  0.058824 
 0.411765  0.176471  0.176471  0.235294 
 0.058824  0.705882  0.176471  0.058824 
 0.235294  0.235294  0.352941  0.176471 
 0.764706  0.000000  0.176471  0.058824 
 0.117647  0.294118  0.176471  0.411765 
 0.294118  0.117647  0.294118  0.294118 
 0.000000  0.176471  0.000000  0.823529 
 0.058824  0.941176  0.000000  0.000000 
 0.882353  0.000000  0.058824  0.058824 
 0.000000  1.000000  0.000000  0.000000 
 0.941176  0.000000  0.058824  0.000000 
 0.411765  0.411765  0.000000  0.176471 
--------------------------------------------------------------------------------

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	Motif WWTAYKTGAWCNAYDTCACAM MEME-1 regular expression
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[TA][AT][TA]A[TC][GT][TC][GA][AC][AT]C[GAC]A[TC][AGT]TCACA[AC]
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Time  0.47 secs.

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MOTIF ASGRGSMRGRAGSAT MEME-2	width =  15  sites =   3  llr = 53  E-value = 3.0e+004
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	Motif ASGRGSMRGRAGSAT MEME-2 Description
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Simplified        A  a::7::33:3a::a:
pos.-specific     C  :3:::77:::::3::
probability       G  :7a3a3:7a7:a7::
matrix            T  ::::::::::::::a

         bits    2.4   * *   *  *   
                 2.1   * *   *  *   
                 1.9   * *   *  *   
                 1.6 * * *   * ** **
Relative         1.4 *** **  * *****
Entropy          1.2 *** ***********
(25.3 bits)      0.9 ***************
                 0.7 ***************
                 0.5 ***************
                 0.2 ***************
                 0.0 ---------------

Multilevel           AGGAGCCGGGAGGAT
consensus             C G GAA A  C  
sequence                            
                                    
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	Motif ASGRGSMRGRAGSAT MEME-2 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
malk                         +      3  1.01e-09         GG AGGAGGCGGGAGGAT GAGAACACGG
male                         +     52  1.51e-08 GGTGGGGCGT AGGGGCAAGGAGGAT GGAAAGAGGT
lac                          -     55  1.51e-08 CACACAACAT ACGAGCCGGAAGCAT AAAGTGTAAA
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	Motif ASGRGSMRGRAGSAT MEME-2 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
malk                                1e-09  2_[+2]_88
male                              1.5e-08  51_[+2]_39
lac                               1.5e-08  54_[-2]_36
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	Motif ASGRGSMRGRAGSAT MEME-2 in BLOCKS format
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BL   MOTIF ASGRGSMRGRAGSAT width=15 seqs=3
malk                     (    3) AGGAGGCGGGAGGAT  1 
male                     (   52) AGGGGCAAGGAGGAT  1 
lac                      (   55) ACGAGCCGGAAGCAT  1 
//

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	Motif ASGRGSMRGRAGSAT MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 15 n= 1638 bayes= 9.09011 E= 3.0e+004 
   171   -823   -823   -823 
  -823     77    176   -823 
  -823   -823    235   -823 
   113   -823     77   -823 
  -823   -823    235   -823 
  -823    176     77   -823 
    13    176   -823   -823 
    13   -823    176   -823 
  -823   -823    235   -823 
    13   -823    176   -823 
   171   -823   -823   -823 
  -823   -823    235   -823 
  -823     77    176   -823 
   171   -823   -823   -823 
  -823   -823   -823    171 
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	Motif ASGRGSMRGRAGSAT MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 15 nsites= 3 E= 3.0e+004 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.333333  0.666667  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.666667  0.000000  0.333333  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.666667  0.333333  0.000000 
 0.333333  0.666667  0.000000  0.000000 
 0.333333  0.000000  0.666667  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.333333  0.000000  0.666667  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.333333  0.666667  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

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	Motif ASGRGSMRGRAGSAT MEME-2 regular expression
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A[GC]G[AG]G[CG][CA][GA]G[GA]AG[GC]AT
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Time  1.02 secs.

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SUMMARY OF MOTIFS
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	Combined block diagrams: non-overlapping sites with p-value < 0.0001
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SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
ce1cg                            7.17e-04  18_[-1(4.24e-07)]_20_[+1(1.47e-06)]_\
    25
ara                              1.54e-05  53_[+1(6.23e-09)]_31
bglr1                            1.56e-01  105
crp                              6.93e-04  61_[+1(8.96e-07)]_23
cya                              8.11e-04  51_[-1(1.77e-06)]_33
deop2                            1.97e-03  5_[+1(1.47e-06)]_79
gale                             8.72e-03  40_[+1(6.82e-06)]_44
ilv                              8.84e-03  37_[+1(6.82e-06)]_47
lac                              1.81e-08  10_[-1(8.55e-06)]_23_[-2(1.51e-08)]_\
    5_[-1(1.77e-06)]_10
male                             2.16e-08  12_[+1(2.13e-06)]_18_[+2(1.51e-08)]_\
    39
malk                             4.60e-09  2_[+2(1.01e-09)]_45_[-1(6.32e-06)]_\
    22
malt                             1.46e-03  42_[-1(8.96e-07)]_42
ompa                             1.12e-03  46_[+1(8.08e-07)]_38
tnaa                             2.46e-03  72_[-1(4.60e-06)]_12
uxu1                             2.06e-03  18_[-1(1.33e-06)]_66
pbr322                           4.05e-04  54_[-1(5.29e-07)]_30
trn9cat                          7.68e-01  105
tdc                              1.16e-01  105
--------------------------------------------------------------------------------

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Stopped because requested number of motifs (2) found.
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CPU: Timothys-iMac.local

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