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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= Primary sequences shuffled preserving 2-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/meme42 -mod zoops -dna -revcomp -nmotifs 2 -objfun nz -w 12 -hsfrac 0.5 -shuf 2 -nostatus 

model:  mod=         zoops    nmotifs=         2    evt=           inf
objective function:           em=       Noise-injected 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=        0.5
        searchsize=   1890    norand=         no    csites=         -1
Letter frequencies in dataset:
A 0.307 C 0.193 G 0.193 T 0.307 
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 GCWTCKKTGSRG MEME-1	width =  12  sites =  17  llr = 102  p-value = 2.6e-001  E-value = 2.9e-001
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	Motif GCWTCKKTGSRG MEME-1 Description
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Simplified        A  21521:111131
pos.-specific     C  28:19:111411
probability       G  512::4515448
matrix            T  11361647222:

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

Multilevel           GCATCTGTGGGG
consensus            A TA GT TCA 
sequence                         
                                 
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	Motif GCWTCKKTGSRG MEME-1 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                Site  
-------------            ------  ----- ---------            ------------
pbr322                       -     65  6.12e-08 TTCTCCTTAC GCATCTGTGCGG TATTTCACAC
male                         +     37  1.70e-06 ATCACACAAA GCGACGGTGGGG CGTAGGGGCA
ilv                          +      1  2.28e-05          . GCTCCGGCGGGG TTTTTTGTTA
ce1cg                        +     24  3.75e-05 GGTTTTTGTG GCATCGGGCGAG AATAGCGCGT
uxu1                         -     90  1.37e-04       GCTT GCATCGGATGAG ATGGCGTATA
malt                         +      6  1.68e-04      GATCA GCGTCGTTTTAG GTGAGTTGTT
malk                         +     27  3.70e-04 TGAGAACACG GCTTCTGTGAAC TAAACCGAGG
tnaa                         -     64  4.44e-04 AATCGAATCA CAATCGTTCGGG GAGCAATATT
gale                         +     67  4.44e-04 CACACTTTTC GCATCTTTGTTA TGCTATGGTT
ompa                         +     81  4.93e-04 TAAGTTTTCA ACTACGTTGTAG ACTTTACATC
trn9cat                      +     70  6.96e-04 AAGCCCTGGG CCAACTTTTGGC GAAAATGAGA
crp                          -     90  1.61e-03       GCTA TCAACTGTACTG CACGGTAATG
cya                          +     28  2.32e-03 TGTAGCGCAT CTTTCTTTACGG TCAATCAGCA
deop2                        -     87  3.13e-03    TATTCTA ACATCTACTCCG CAACACACTT
tdc                          -     90  3.82e-03       AACA GGATATGTGCGA CCACTCACAA
lac                          -     35  3.82e-03 ATAAAGTGTA AAGCCTGGGGTG CCTAATGAGT
ara                          -     34  5.00e-03 ATCAATGTGG ACTTTTCTGCCG TGATTATAGA
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	Motif GCWTCKKTGSRG MEME-1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
pbr322                            6.1e-08  64_[-1]_29
male                              1.7e-06  36_[+1]_57
ilv                               2.3e-05  [+1]_93
ce1cg                             3.8e-05  23_[+1]_70
uxu1                              0.00014  89_[-1]_4
malt                              0.00017  5_[+1]_88
malk                              0.00037  26_[+1]_67
tnaa                              0.00044  63_[-1]_30
gale                              0.00044  66_[+1]_27
ompa                              0.00049  80_[+1]_13
trn9cat                            0.0007  69_[+1]_24
crp                                0.0016  89_[-1]_4
cya                                0.0023  27_[+1]_66
deop2                              0.0031  86_[-1]_7
tdc                                0.0038  89_[-1]_4
lac                                0.0038  34_[-1]_59
ara                                 0.005  33_[-1]_60
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	Motif GCWTCKKTGSRG MEME-1 in BLOCKS format
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BL   MOTIF GCWTCKKTGSRG width=12 seqs=17
pbr322                   (   65) GCATCTGTGCGG  1 
male                     (   37) GCGACGGTGGGG  1 
ilv                      (    1) GCTCCGGCGGGG  1 
ce1cg                    (   24) GCATCGGGCGAG  1 
uxu1                     (   90) GCATCGGATGAG  1 
malt                     (    6) GCGTCGTTTTAG  1 
malk                     (   27) GCTTCTGTGAAC  1 
tnaa                     (   64) CAATCGTTCGGG  1 
gale                     (   67) GCATCTTTGTTA  1 
ompa                     (   81) ACTACGTTGTAG  1 
trn9cat                  (   70) CCAACTTTTGGC  1 
crp                      (   90) TCAACTGTACTG  1 
cya                      (   28) CTTTCTTTACGG  1 
deop2                    (   87) ACATCTACTCCG  1 
tdc                      (   90) GGATATGTGCGA  1 
lac                      (   35) AAGCCTGGGGTG  1 
ara                      (   34) ACTTTTCTGCCG  1 
//

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	Motif GCWTCKKTGSRG MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 2444 bayes= 8.39832 E= 2.9e-001 
   -37    -15    143   -237 
  -137    196   -173   -237 
    80  -1073    -15     -5 
   -37    -73  -1073    109 
  -237    217  -1073   -237 
 -1073  -1073    107     95 
  -237   -173    143     21 
  -237    -73    -73    121 
  -137    -73    143    -37 
  -237     85    107    -78 
    -5    -73    107    -78 
  -137    -73    196  -1073 
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	Motif GCWTCKKTGSRG MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 17 E= 2.9e-001 
 0.235294  0.176471  0.529412  0.058824 
 0.117647  0.764706  0.058824  0.058824 
 0.529412  0.000000  0.176471  0.294118 
 0.235294  0.117647  0.000000  0.647059 
 0.058824  0.882353  0.000000  0.058824 
 0.000000  0.000000  0.411765  0.588235 
 0.058824  0.058824  0.529412  0.352941 
 0.058824  0.117647  0.117647  0.705882 
 0.117647  0.117647  0.529412  0.235294 
 0.058824  0.352941  0.411765  0.176471 
 0.294118  0.117647  0.411765  0.176471 
 0.117647  0.117647  0.764706  0.000000 
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	Motif GCWTCKKTGSRG MEME-1 regular expression
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[GA]C[AT][TA]C[TG][GT]T[GT][GC][GA]G
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Time  0.56 secs.

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MOTIF RCRBATAAMAAA MEME-2	width =  12  sites =  14  llr = 119  p-value = 2.7e-001  E-value = 3.1e-001
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	Motif RCRBATAAMAAA MEME-2 Description
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Simplified        A  51418:9969a7
pos.-specific     C  18:4:21:4::1
probability       G  4:621::::1::
matrix            T  :11318:1:::2

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

Multilevel           ACGCATAAAAAA
consensus            G AT C  C  T
sequence                G        
                                 
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	Motif RCRBATAAMAAA MEME-2 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                Site  
-------------            ------  ----- ---------            ------------
gale                         +      1  2.85e-07          . GCGCATAAAAAA CGGCTAAATT
malt                         +     65  2.77e-06 GCAAATTCAG ACACATAAAAAA ACGTCATCGC
ilv                          -     16  3.56e-06 GTACTGAATT GCAGATAACAAA AAACCCCGCC
lac                          +     89  6.60e-06 GGAATTGTGA GCGGATAACAAT TTCAC     
ara                          +      8  8.68e-06    GACAAAA ACGCGTAACAAA AGTGTCTATA
deop2                        -     61  4.59e-05 ACACTTCGAT ACACATCACAAT TAAGGAAATC
malk                         -     93  4.95e-05          T GCGCACATAAAA TCGCCACGAT
bglr1                        -     29  7.12e-05 TTATAAAGTT ATATATAACAAA TCCCAATAAT
male                         +     79  8.24e-05 AAAGAGGTTG CCGTATAAAGAA ACTAGAGTCC
ompa                         +      1  8.77e-05          . GCTGACAAAAAA GATTAAACAT
tnaa                         -      1  1.67e-04 AAGAATTTTA ATGTTTAAAAAA           
uxu1                         -     18  1.77e-04 ATTGGGTTAA CCACATCACAAC AATTTCACTC
ce1cg                        -     61  1.77e-04 TTTTGTGAAA ACGATCAAAAAA ACAGTCTTTC
tdc                          -      2  1.89e-04 CAACAAGTTA AAGTATAAAAAT C         
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	Motif RCRBATAAMAAA MEME-2 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
gale                              2.8e-07  [+2]_93
malt                              2.8e-06  64_[+2]_29
ilv                               3.6e-06  15_[-2]_78
lac                               6.6e-06  88_[+2]_5
ara                               8.7e-06  7_[+2]_86
deop2                             4.6e-05  60_[-2]_33
malk                                5e-05  92_[-2]_1
bglr1                             7.1e-05  28_[-2]_65
male                              8.2e-05  78_[+2]_15
ompa                              8.8e-05  [+2]_93
tnaa                              0.00017  [-2]_93
uxu1                              0.00018  17_[-2]_76
ce1cg                             0.00018  60_[-2]_33
tdc                               0.00019  1_[-2]_92
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	Motif RCRBATAAMAAA MEME-2 in BLOCKS format
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BL   MOTIF RCRBATAAMAAA width=12 seqs=14
gale                     (    1) GCGCATAAAAAA  1 
malt                     (   65) ACACATAAAAAA  1 
ilv                      (   16) GCAGATAACAAA  1 
lac                      (   89) GCGGATAACAAT  1 
ara                      (    8) ACGCGTAACAAA  1 
deop2                    (   61) ACACATCACAAT  1 
malk                     (   93) GCGCACATAAAA  1 
bglr1                    (   29) ATATATAACAAA  1 
male                     (   79) CCGTATAAAGAA  1 
ompa                     (    1) GCTGACAAAAAA  1 
tnaa                     (    1) ATGTTTAAAAAA  1 
uxu1                     (   18) CCACATCACAAC  1 
ce1cg                    (   61) ACGATCAAAAAA  1 
tdc                      (    2) AAGTATAAAAAT  1 
//

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	Motif RCRBATAAMAAA MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 2444 bayes= 7.08163 E= 3.1e-001 
    72    -46     87  -1045 
  -209    200  -1045   -109 
    23  -1045    154   -209 
  -209    113     13     -9 
   137  -1045   -145   -109 
 -1045     13  -1045    137 
   149    -46  -1045  -1045 
   161  -1045  -1045   -209 
    91    113  -1045  -1045 
   161  -1045   -145  -1045 
   172  -1045  -1045  -1045 
   123   -145  -1045    -50 
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	Motif RCRBATAAMAAA MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 14 E= 3.1e-001 
 0.500000  0.142857  0.357143  0.000000 
 0.071429  0.785714  0.000000  0.142857 
 0.357143  0.000000  0.571429  0.071429 
 0.071429  0.428571  0.214286  0.285714 
 0.785714  0.000000  0.071429  0.142857 
 0.000000  0.214286  0.000000  0.785714 
 0.857143  0.142857  0.000000  0.000000 
 0.928571  0.000000  0.000000  0.071429 
 0.571429  0.428571  0.000000  0.000000 
 0.928571  0.000000  0.071429  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.714286  0.071429  0.000000  0.214286 
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	Motif RCRBATAAMAAA MEME-2 regular expression
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[AG]C[GA][CTG]A[TC]AA[AC]AA[AT]
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Time  0.82 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                            2.16e-03  23_[+1(3.75e-05)]_70
ara                              7.87e-03  7_[+2(8.68e-06)]_71_[-2(9.37e-05)]_\
    3
bglr1                            6.25e-02  28_[-2(7.12e-05)]_65
crp                              2.43e-01  105
cya                              4.76e-01  105
deop2                            2.51e-02  60_[-2(4.59e-05)]_33
gale                             5.73e-05  [+2(2.85e-07)]_93
ilv                              3.94e-05  [+1(2.28e-05)]_3_[-2(3.56e-06)]_78
lac                              5.31e-03  88_[+2(6.60e-06)]_5
male                             6.49e-05  36_[+1(1.70e-06)]_30_[+2(8.24e-05)]_\
    15
malk                             5.22e-03  92_[-2(4.95e-05)]_1
malt                             1.95e-04  64_[+2(2.77e-06)]_29
ompa                             1.09e-02  [+2(8.77e-05)]_93
tnaa                             1.73e-02  105
uxu1                             6.75e-03  105
pbr322                           1.37e-04  64_[-1(6.12e-08)]_29
trn9cat                          3.14e-01  105
tdc                              8.99e-02  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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