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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/crp0.s
CONTROL SEQUENCES= Primary sequences shuffled preserving 3-mers
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/meme21 -mod anr -dna -revcomp -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus 

model:  mod=           anr    nmotifs=         2    evt=           inf
objective function:           em=       Differential Enrichment mHG
                              starts=   log likelihood ratio (LLR)
strands: + -
width:  minw=           12    maxw=           12
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
data:   n=            1890    N=              18
sample: seed=            0    hsfrac=        0.6
        searchsize=   1890    norand=         no    csites=         -1
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 HCAVMTCACAWW MEME-1	width =  12  sites =  17  llr = 134  p-value = 6.6e-001  E-value = 6.6e-001
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	Motif HCAVMTCACAWW MEME-1 Description
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Simplified        A  5:746118:944
pos.-specific     C  381442919111
probability       G  :122:1:11:1:
matrix            T  21:::6::::46

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

Multilevel           ACACATCACAAT
consensus            C  AC     TA
sequence             T  G        
                                 
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	Motif HCAVMTCACAWW MEME-1 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                Site  
-------------            ------  ----- ---------            ------------
deop2                        -     61  1.77e-07 ACACTTCGAT ACACATCACAAT TAAGGAAATC
uxu1                         -     18  1.52e-05 ATTGGGTTAA CCACATCACAAC AATTTCACTC
bglr1                        -     22  2.04e-05 GTTATATATA ACAAATCCCAAT AATTAAGTTA
bglr1                        +      1  2.04e-05          . ACAAATCCCAAT AACTTAATTA
deop2                        +     16  2.32e-05 ATTATTTGAA CCAGATCGCATT ACAGTGATGC
tnaa                         -     72  2.66e-05 TAAATGTGAA TCGAATCACAAT CGTTCGGGGA
tdc                          -     79  4.33e-05 GATATGTGCG ACCACTCACAAA TTAACTTTCA
lac                          -     82  4.33e-05 GAAATTGTTA TCCGCTCACAAT TCCACACAAC
malt                         -     15  6.45e-05 ATCTTTATTA ACAACTCACCTA AAACGACGCT
lac                          -     10  9.21e-05 AATGAGTGAG CTAACTCACATT AATTGCGTT 
pbr322                       -     49  1.18e-04 GTGCGGTATT TCACACCGCATA TGGTGCACTC
deop2                        -     78  1.89e-04 AACATCTACT CCGCAACACACT TCGATACACA
male                         -     40  2.18e-04 CCTTGCCCCT ACGCCCCACCGT CGCTTTGTGT
male                         +     23  2.50e-04 ATTCTGTAAC AGAGATCACACA AAGCGACGGT
lac                          -     69  3.10e-04 GCTCACAATT CCACACAACATA CGAGCCGGAA
pbr322                       +     62  3.99e-04 GCGGTGTGAA ATACCGCACAGA TGCGTAAGGA
pbr322                       +     20  4.53e-04 CTATGCGGCA TCAGAGCAGATT GTACTGAGAG
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	Motif HCAVMTCACAWW MEME-1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
deop2                             0.00019  15_[+1]_33_[-1]_5_[-1]_16
uxu1                              1.5e-05  17_[-1]_76
bglr1                               2e-05  [+1]_9_[-1]_72
tnaa                              2.7e-05  71_[-1]_22
tdc                               4.3e-05  78_[-1]_15
lac                               0.00031  9_[-1]_47_[-1]_1_[-1]_12
malt                              6.4e-05  14_[-1]_79
pbr322                            0.00045  19_[+1]_17_[-1]_1_[+1]_32
male                              0.00022  22_[+1]_5_[-1]_54
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	Motif HCAVMTCACAWW MEME-1 in BLOCKS format
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BL   MOTIF HCAVMTCACAWW width=12 seqs=17
deop2                    (   61) ACACATCACAAT  1 
uxu1                     (   18) CCACATCACAAC  1 
bglr1                    (   22) ACAAATCCCAAT  1 
bglr1                    (    1) ACAAATCCCAAT  1 
deop2                    (   16) CCAGATCGCATT  1 
tnaa                     (   72) TCGAATCACAAT  1 
tdc                      (   79) ACCACTCACAAA  1 
lac                      (   82) TCCGCTCACAAT  1 
malt                     (   15) ACAACTCACCTA  1 
lac                      (   10) CTAACTCACATT  1 
pbr322                   (   49) TCACACCGCATA  1 
deop2                    (   78) CCGCAACACACT  1 
male                     (   40) ACGCCCCACCGT  1 
male                     (   23) AGAGATCACACA  1 
lac                      (   69) CCACACAACATA  1 
pbr322                   (   62) ATACCGCACAGA  1 
pbr322                   (   20) TCAGAGCAGATT  1 
//

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	Motif HCAVMTCACAWW MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 7.30945 E= 6.6e-001 
    63     59  -1073    -37 
 -1073    207   -173   -137 
   121    -73    -15  -1073 
    21    107     26  -1073 
   109     85  -1073  -1073 
  -237    -15    -73    109 
  -237    226  -1073  -1073 
   133    -73    -73  -1073 
 -1073    226   -173  -1073 
   154    -73  -1073  -1073 
    44    -73    -73     21 
    21   -173  -1073     95 
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	Motif HCAVMTCACAWW MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 17 E= 6.6e-001 
 0.470588  0.294118  0.000000  0.235294 
 0.000000  0.823529  0.058824  0.117647 
 0.705882  0.117647  0.176471  0.000000 
 0.352941  0.411765  0.235294  0.000000 
 0.647059  0.352941  0.000000  0.000000 
 0.058824  0.176471  0.117647  0.647059 
 0.058824  0.941176  0.000000  0.000000 
 0.764706  0.117647  0.117647  0.000000 
 0.000000  0.941176  0.058824  0.000000 
 0.882353  0.117647  0.000000  0.000000 
 0.411765  0.117647  0.117647  0.352941 
 0.352941  0.058824  0.000000  0.588235 
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	Motif HCAVMTCACAWW MEME-1 regular expression
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[ACT]CA[CAG][AC]TCACA[AT][TA]
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Time  0.25 secs.

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MOTIF ATMAMSAWRYTM MEME-2	width =  12  sites =   6  llr = 62  p-value = 4.9e-001  E-value = 4.9e-001
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	Motif ATMAMSAWRYTM MEME-2 Description
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Simplified        A  a:5a52a55::5
pos.-specific     C  ::3:53:::7:5
probability       G  ::2::5::5:::
matrix            T  :a:::::5:3a:

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

Multilevel           ATAAAGAAACTA
consensus              C CC TGT C
sequence                         
                                 
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	Motif ATMAMSAWRYTM MEME-2 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                Site  
-------------            ------  ----- ---------            ------------
tdc                          +     47  1.52e-06 TTTAATTGTA ATAACGATACTC TGGAAAGTAT
bglr1                        -     82  4.41e-06 TGATAAAAAT ATGACCATGCTC ACAGTTATTA
male                         +     83  7.68e-06 AGGTTGCCGT ATAAAGAAACTA GAGTCCGTTT
malk                         -     58  1.01e-05 TGCAAGCAAC ATCACGAAATTC CTTACATGAC
tdc                          -     14  2.22e-05 ACCTTTAAAT ATCAACAAGTTA AAGTATAAAA
ara                          -     87  2.58e-05    CTTATGG ATAAAAATGCTA TGGCATAGCA
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	Motif ATMAMSAWRYTM MEME-2 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
tdc                               2.2e-05  13_[-2]_21_[+2]_47
bglr1                             4.4e-06  81_[-2]_12
male                              7.7e-06  82_[+2]_11
malk                                1e-05  57_[-2]_36
ara                               2.6e-05  86_[-2]_7
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	Motif ATMAMSAWRYTM MEME-2 in BLOCKS format
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BL   MOTIF ATMAMSAWRYTM width=12 seqs=6
tdc                      (   47) ATAACGATACTC  1 
bglr1                    (   82) ATGACCATGCTC  1 
male                     (   83) ATAAAGAAACTA  1 
malk                     (   58) ATCACGAAATTC  1 
tdc                      (   14) ATCAACAAGTTA  1 
ara                      (   87) ATAAAAATGCTA  1 
//

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	Motif ATMAMSAWRYTM MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 8.58325 E= 4.9e-001 
   172   -923   -923   -923 
  -923   -923   -923    172 
    72     77    -23   -923 
   172   -923   -923   -923 
    72    135   -923   -923 
   -87     77    135   -923 
   172   -923   -923   -923 
    72   -923   -923     72 
    72   -923    135   -923 
  -923    177   -923     13 
  -923   -923   -923    172 
    72    135   -923   -923 
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	Motif ATMAMSAWRYTM MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 6 E= 4.9e-001 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.500000  0.333333  0.166667  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.166667  0.333333  0.500000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  0.666667  0.000000  0.333333 
 0.000000  0.000000  0.000000  1.000000 
 0.500000  0.500000  0.000000  0.000000 
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	Motif ATMAMSAWRYTM MEME-2 regular expression
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AT[AC]A[AC][GC]A[AT][AG][CT]T[AC]
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Time  0.45 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                            7.25e-01  105
ara                              1.54e-02  86_[-2(2.58e-05)]_7
bglr1                            4.34e-05  [+1(2.04e-05)]_9_[-1(2.04e-05)]_48_\
    [-2(4.41e-06)]_12
crp                              3.95e-01  105
cya                              5.40e-01  105
deop2                            2.75e-04  15_[+1(2.32e-05)]_33_[-1(1.77e-07)]_\
    33
gale                             3.62e-01  105
ilv                              6.56e-01  105
lac                              3.34e-02  9_[-1(9.21e-05)]_60_[-1(4.33e-05)]_\
    12
male                             6.23e-04  82_[+2(7.68e-06)]_11
malk                             1.00e-02  57_[-2(1.01e-05)]_36
malt                             4.08e-02  14_[-1(6.45e-05)]_79
ompa                             5.32e-01  105
tnaa                             1.69e-02  71_[-1(2.66e-05)]_22
uxu1                             1.30e-02  17_[-1(1.52e-05)]_76
pbr322                           1.04e-01  105
trn9cat                          6.93e-01  105
tdc                              3.24e-05  13_[-2(2.22e-05)]_21_[+2(1.52e-06)]_\
    20_[-1(4.33e-05)]_15
--------------------------------------------------------------------------------

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

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