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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/meme43 -mod anr -dna -revcomp -nmotifs 2 -objfun nz -w 12 -hsfrac 0.5 -shuf 2 -nostatus 

model:  mod=           anr    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 AKTGTGATBYGB MEME-1	width =  12  sites =  15  llr = 136  p-value = 8.1e-001  E-value = 1.4e+000
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	Motif AKTGTGATBYGB MEME-1 Description
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Simplified        A  71::::911::1
pos.-specific     C  ::::1::33333
probability       G  13:a18::4:73
matrix            T  25a:821727:3

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

Multilevel           ATTGTGATGTGG
consensus            TG   T CCCCT
sequence                     T  C
                                 
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	Motif AKTGTGATBYGB MEME-1 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                Site  
-------------            ------  ----- ---------            ------------
deop2                        +     61  7.81e-07 GATTTCCTTA ATTGTGATGTGT ATCGAAGTGT
ara                          -     64  7.10e-06 GGCATAGCAA AGTGTGACGCCG TGCAAATAAT
uxu1                         +     18  7.87e-06 GAGTGAAATT GTTGTGATGTGG TTAACCCAAT
lac                          -     89  1.74e-05      GTGAA ATTGTTATCCGC TCACAATTCC
gale                         -     51  2.13e-05 AGATGCGAAA AGTGTGACATGG AATAAATTAG
deop2                        +     78  2.32e-05 TGTGTATCGA AGTGTGTTGCGG AGTAGATGTT
bglr1                        +     22  2.54e-05 TAACTTAATT ATTGGGATTTGT TATATATAAC
bglr1                        -      1  2.54e-05 TAATTAAGTT ATTGGGATTTGT           
male                         -     23  2.80e-05 ACCGTCGCTT TGTGTGATCTCT GTTACAGAAT
crp                          -     72  3.31e-05 ACTGCACGGT AATGTGACGTCC TTTGCATACA
tnaa                         +     72  4.22e-05 TCCCCGAACG ATTGTGATTCGA TTCACATTTA
deop2                        -     16  4.61e-05 GCATCACTGT AATGCGATCTGG TTCAAATAAT
ilv                          +     16  5.02e-05 GGCGGGGTTT TTTGTTATCTGC AATTCAGTAC
ompa                         -     57  5.89e-05 AAAACTTACA AGTGTGAACTCC GTCAGGCATA
ara                          -      8  9.53e-05 TATAGACACT TTTGTTACGCGT TTTTGTC   
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	Motif AKTGTGATBYGB MEME-1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
deop2                             4.6e-05  15_[-1]_33_[+1]_5_[+1]_16
ara                               9.5e-05  7_[-1]_44_[-1]_30
uxu1                              7.9e-06  17_[+1]_76
lac                               1.7e-05  88_[-1]_5
gale                              2.1e-05  50_[-1]_43
bglr1                             2.5e-05  [-1]_9_[+1]_72
male                              2.8e-05  22_[-1]_71
crp                               3.3e-05  71_[-1]_22
tnaa                              4.2e-05  71_[+1]_22
ilv                                 5e-05  15_[+1]_78
ompa                              5.9e-05  56_[-1]_37
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	Motif AKTGTGATBYGB MEME-1 in BLOCKS format
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BL   MOTIF AKTGTGATBYGB width=12 seqs=15
deop2                    (   61) ATTGTGATGTGT  1 
ara                      (   64) AGTGTGACGCCG  1 
uxu1                     (   18) GTTGTGATGTGG  1 
lac                      (   89) ATTGTTATCCGC  1 
gale                     (   51) AGTGTGACATGG  1 
deop2                    (   78) AGTGTGTTGCGG  1 
bglr1                    (   22) ATTGGGATTTGT  1 
bglr1                    (    1) ATTGGGATTTGT  1 
male                     (   23) TGTGTGATCTCT  1 
crp                      (   72) AATGTGACGTCC  1 
tnaa                     (   72) ATTGTGATTCGA  1 
deop2                    (   16) AATGCGATCTGG  1 
ilv                      (   16) TTTGTTATCTGC  1 
ompa                     (   57) AGTGTGAACTCC  1 
ara                      (    8) TTTGTTACGCGT  1 
//

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	Motif AKTGTGATBYGB MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 2444 bayes= 8.08695 E= 1.4e+000 
   127  -1055   -155    -60 
  -119  -1055     77     81 
 -1055  -1055  -1055    172 
 -1055  -1055    235  -1055 
 -1055   -155    -55    139 
 -1055  -1055    203    -60 
   162  -1055  -1055   -219 
  -219     44  -1055    113 
  -219     77    103    -60 
 -1055     77  -1055    113 
 -1055     44    190  -1055 
  -219     44     77     13 
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	Motif AKTGTGATBYGB MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 15 E= 1.4e+000 
 0.733333  0.000000  0.066667  0.200000 
 0.133333  0.000000  0.333333  0.533333 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.066667  0.133333  0.800000 
 0.000000  0.000000  0.800000  0.200000 
 0.933333  0.000000  0.000000  0.066667 
 0.066667  0.266667  0.000000  0.666667 
 0.066667  0.333333  0.400000  0.200000 
 0.000000  0.333333  0.000000  0.666667 
 0.000000  0.266667  0.733333  0.000000 
 0.066667  0.266667  0.333333  0.333333 
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	Motif AKTGTGATBYGB MEME-1 regular expression
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[AT][TG]TGT[GT]A[TC][GCT][TC][GC][GTC]
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Time  0.42 secs.

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MOTIF AAAAAACGKCWT MEME-2	width =  12  sites =   8  llr = 81  p-value = 9.6e-001  E-value = 2.2e+000
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	Motif AAAAAACGKCWT MEME-2 Description
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Simplified        A  96aa893:::51
pos.-specific     C  11::1181:8::
probability       G  :1:::::943::
matrix            T  :1::1:::6:59

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

Multilevel           AAAAAACGTCAT
consensus                  A GGT 
sequence                         
                                 
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	Motif AAAAAACGKCWT MEME-2 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                Site  
-------------            ------  ----- ---------            ------------
malt                         +     72  3.34e-07 CAGACACATA AAAAAACGTCAT CGCTTGCATT
ompa                         -     32  3.11e-06 AGGCATATGA AAAAAAAGTCTT GTATAAGGTA
gale                         +      7  5.92e-06     GCGCAT AAAAAACGGCTA AATTCTTGTG
ilv                          +     36  6.35e-06 GCAATTCAGT ACAAAACGTGAT CAACCCCTCA
malk                         +     19  9.33e-06 CGGGAGGATG AGAACACGGCTT CTGTGAACTA
ce1cg                        -     53  1.61e-05 AAACGATCAA AAAAACAGTCTT TCACACCACG
pbr322                       +     85  2.94e-05 GCGTAAGGAG AAAATACCGCAT CAGGCGCTC 
cya                          -     63  3.72e-05 AAAAAATGGT CTAAAACGTGAT CAATTTAACA
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	Motif AAAAAACGKCWT MEME-2 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
malt                              3.3e-07  71_[+2]_22
ompa                              3.1e-06  31_[-2]_62
gale                              5.9e-06  6_[+2]_87
ilv                               6.3e-06  35_[+2]_58
malk                              9.3e-06  18_[+2]_75
ce1cg                             1.6e-05  52_[-2]_41
pbr322                            2.9e-05  84_[+2]_9
cya                               3.7e-05  62_[-2]_31
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	Motif AAAAAACGKCWT MEME-2 in BLOCKS format
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BL   MOTIF AAAAAACGKCWT width=12 seqs=8
malt                     (   72) AAAAAACGTCAT  1 
ompa                     (   32) AAAAAAAGTCTT  1 
gale                     (    7) AAAAAACGGCTA  1 
ilv                      (   36) ACAAAACGTGAT  1 
malk                     (   19) AGAACACGGCTT  1 
ce1cg                    (   53) AAAAACAGTCTT  1 
pbr322                   (   85) AAAATACCGCAT  1 
cya                      (   63) CTAAAACGTGAT  1 
//

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	Motif AAAAAACGKCWT MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 2444 bayes= 7.71768 E= 2.2e+000 
   152    -65   -965   -965 
   104    -65    -65   -128 
   172   -965   -965   -965 
   172   -965   -965   -965 
   130    -65   -965   -128 
   152    -65   -965   -965 
   -28    194   -965   -965 
  -965    -65    216   -965 
  -965   -965     94    104 
  -965    194     35   -965 
    72   -965   -965     72 
  -128   -965   -965    152 
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	Motif AAAAAACGKCWT MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 8 E= 2.2e+000 
 0.875000  0.125000  0.000000  0.000000 
 0.625000  0.125000  0.125000  0.125000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.750000  0.125000  0.000000  0.125000 
 0.875000  0.125000  0.000000  0.000000 
 0.250000  0.750000  0.000000  0.000000 
 0.000000  0.125000  0.875000  0.000000 
 0.000000  0.000000  0.375000  0.625000 
 0.000000  0.750000  0.250000  0.000000 
 0.500000  0.000000  0.000000  0.500000 
 0.125000  0.000000  0.000000  0.875000 
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	Motif AAAAAACGKCWT MEME-2 regular expression
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AAAAAA[CA]G[TG][CG][AT]T
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Time  0.67 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                            1.05e-02  52_[-2(1.61e-05)]_41
ara                              1.92e-03  7_[-1(9.53e-05)]_44_[-1(7.10e-06)]_\
    30
bglr1                            1.94e-02  [-1(2.54e-05)]_9_[+1(2.54e-05)]_72
crp                              2.63e-02  71_[-1(3.31e-05)]_22
cya                              2.88e-02  62_[-2(3.72e-05)]_31
deop2                            1.30e-03  15_[-1(4.61e-05)]_33_[+1(7.81e-07)]_\
    5_[+1(2.32e-05)]_16
gale                             5.92e-05  6_[+2(5.92e-06)]_32_[-1(2.13e-05)]_\
    43
ilv                              1.39e-04  15_[+1(5.02e-05)]_8_[+2(6.35e-06)]_\
    58
lac                              2.06e-02  88_[-1(1.74e-05)]_5
male                             2.88e-02  22_[-1(2.80e-05)]_71
malk                             7.84e-03  18_[+2(9.33e-06)]_75
malt                             1.98e-04  71_[+2(3.34e-07)]_22
ompa                             8.34e-05  31_[-2(3.11e-06)]_13_[-1(5.89e-05)]_\
    37
tnaa                             2.60e-02  71_[+1(4.22e-05)]_22
uxu1                             2.04e-03  17_[+1(7.87e-06)]_76
pbr322                           2.43e-02  84_[+2(2.94e-05)]_9
trn9cat                          8.83e-01  105
tdc                              7.51e-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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