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MEME - Motif discovery tool
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MEME version 5.4.0 (Release date: Tue Mar 9 17:38:20 2021 -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.

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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 common/crp0.s -oc results/meme41 -mod oops -dna -revcomp -nmotifs 2 -objfun nz -w 12 -hsfrac 0.5 -shuf 2 -nostatus -mpi 

model:  mod=          oops    nmotifs=         2    evt=           inf
objective function:           em=       Noise-injected mHG
                              starts=   log likelihood ratio (LLR)
strands: + -
width:  minw=           12    maxw=           12
nsites: minsites=       18    maxsites=       18    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 DTGTGKMATTGT MEME-1	width =  12  sites =  18  llr = 131  p-value = 4.5e-001  E-value = 4.5e-001
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	Motif DTGTGKMATTGT MEME-1 Description
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Simplified        A  2121216911::
pos.-specific     C  :::2::3132:1
probability       G  318:65::::71
matrix            T  48:7242:6738

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

Multilevel           TTGTGGAATTGT
consensus            G  CTTC CCT 
sequence             A           
                                 
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	Motif DTGTGKMATTGT MEME-1 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                Site  
-------------            ------  ----- ---------            ------------
lac                          +     75  6.94e-08 CTCGTATGTT GTGTGGAATTGT GAGCGGATAA
bglr1                        -     57  9.34e-06 GTTATTAACT TTGTGTAATTTT AGGAATTTAT
gale                         -     32  2.42e-05 TGGAATAAAT TAGTGGAATCGT TTACACAAGA
cya                          -      1  3.81e-05 CTACATACAA GTGTAGCACCGT           
ce1cg                        +     19  5.30e-05 GTGCTGGTTT TTGTGGCATCGG GCGAGAATAG
uxu1                         +      8  8.05e-05    CCCATGA GAGTGAAATTGT TGTGATGTGG
deop2                        -     28  9.82e-05 ACTTACAAGT TTGCATCACTGT AATGCGATCT
ara                          -     40  9.82e-05 CAAATAATCA ATGTGGACTTTT CTGCCGTGAT
tnaa                         -     87  1.09e-04    TCTGAAA TTGTTTAAATGT GAATCGAATC
tdc                          +     34  1.31e-04 ATATTTAAAG GTATTTAATTGT AATAACGATA
pbr322                       -     85  1.31e-04  GAGCGCCTG ATGCGGTATTTT CTCCTTACGC
trn9cat                      +     38  2.08e-04 AAATAAATCC TGGTGTCCCTGT TGATACCGGG
crp                          -     38  2.67e-04 CAGTACATCA ATGTATTACTGT AGCATCCTGA
ompa                         -     11  3.15e-04 TGTATAAGGT ATGTTTAATCTT TTTTGTCAGC
malt                         +     43  3.40e-04 AGATTTGGAA TTGTGACACAGT GCAAATTCAG
male                         -      1  3.97e-04 GTTACAGAAT TGGCGGTAATGT           
ilv                          -     26  6.14e-04 ATCACGTTTT GTACTGAATTGC AGATAACAAA
malk                         +     53  1.82e-03 CCGAGGTCAT GTAAGGAATTTC GTGATGTTGC
--------------------------------------------------------------------------------

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	Motif DTGTGKMATTGT MEME-1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
lac                               6.9e-08  74_[+1]_19
bglr1                             9.3e-06  56_[-1]_37
gale                              2.4e-05  31_[-1]_62
cya                               3.8e-05  [-1]_93
ce1cg                             5.3e-05  18_[+1]_75
uxu1                              8.1e-05  7_[+1]_86
deop2                             9.8e-05  27_[-1]_66
ara                               9.8e-05  39_[-1]_54
tnaa                              0.00011  86_[-1]_7
tdc                               0.00013  33_[+1]_60
pbr322                            0.00013  84_[-1]_9
trn9cat                           0.00021  37_[+1]_56
crp                               0.00027  37_[-1]_56
ompa                              0.00031  10_[-1]_83
malt                              0.00034  42_[+1]_51
male                               0.0004  [-1]_93
ilv                               0.00061  25_[-1]_68
malk                               0.0018  52_[+1]_41
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	Motif DTGTGKMATTGT MEME-1 in BLOCKS format
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BL   MOTIF DTGTGKMATTGT width=12 seqs=18
lac                      (   75) GTGTGGAATTGT  1 
bglr1                    (   57) TTGTGTAATTTT  1 
gale                     (   32) TAGTGGAATCGT  1 
cya                      (    1) GTGTAGCACCGT  1 
ce1cg                    (   19) TTGTGGCATCGG  1 
uxu1                     (    8) GAGTGAAATTGT  1 
deop2                    (   28) TTGCATCACTGT  1 
ara                      (   40) ATGTGGACTTTT  1 
tnaa                     (   87) TTGTTTAAATGT  1 
tdc                      (   34) GTATTTAATTGT  1 
pbr322                   (   85) ATGCGGTATTTT  1 
trn9cat                  (   38) TGGTGTCCCTGT  1 
crp                      (   38) ATGTATTACTGT  1 
ompa                     (   11) ATGTTTAATCTT  1 
malt                     (   43) TTGTGACACAGT  1 
male                     (    1) TGGCGGTAATGT  1 
ilv                      (   26) GTACTGAATTGC  1 
malk                     (   53) GTAAGGAATTTC  1 
//

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	Motif DTGTGKMATTGT MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 2444 bayes= 6.53916 E= 4.5e-001 
   -45  -1081     77     55 
  -145  -1081    -82    135 
   -87  -1081    209  -1081 
  -245     18  -1081    125 
   -87  -1081    164    -45 
  -145  -1081    135     35 
    87     50  -1081    -87 
   155    -82  -1081  -1081 
  -145     50  -1081    101 
  -245     18  -1081    125 
 -1081  -1081    188    -13 
 -1081    -82   -182    145 
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	Motif DTGTGKMATTGT MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 4.5e-001 
 0.222222  0.000000  0.333333  0.444444 
 0.111111  0.000000  0.111111  0.777778 
 0.166667  0.000000  0.833333  0.000000 
 0.055556  0.222222  0.000000  0.722222 
 0.166667  0.000000  0.611111  0.222222 
 0.111111  0.000000  0.500000  0.388889 
 0.555556  0.277778  0.000000  0.166667 
 0.888889  0.111111  0.000000  0.000000 
 0.111111  0.277778  0.000000  0.611111 
 0.055556  0.222222  0.000000  0.722222 
 0.000000  0.000000  0.722222  0.277778 
 0.000000  0.111111  0.055556  0.833333 
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	Motif DTGTGKMATTGT MEME-1 regular expression
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[TGA]TG[TC][GT][GT][AC]A[TC][TC][GT]T
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Time  0.22 secs.

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MOTIF BWSDTCACANWW MEME-2	width =  12  sites =  18  llr = 131  p-value = 1.4e-001  E-value = 1.4e-001
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	Motif BWSDTCACANWW MEME-2 Description
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Simplified        A  1614::8:8243
pos.-specific     C  2132:9:a:3:1
probability       G  4152112:22::
matrix            T  33129::::366

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

Multilevel           GAGATCACATTT
consensus            TTCG    GCAA
sequence             C  T     G  
                                 
--------------------------------------------------------------------------------

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	Motif BWSDTCACANWW MEME-2 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                Site  
-------------            ------  ----- ---------            ------------
ompa                         +     58  7.03e-07 ATGCCTGACG GAGTTCACACTT GTAAGTTTTC
male                         +     24  4.18e-06 TTCTGTAACA GAGATCACACAA AGCGACGGTG
crp                          +     73  1.27e-05 GTATGCAAAG GACGTCACATTA CCGTGCAGTA
ara                          +     65  2.02e-05 TTATTTGCAC GGCGTCACACTT TGCTATGCCA
deop2                        -     60  3.38e-05 CACTTCGATA CACATCACAATT AAGGAAATCT
tdc                          +     86  5.55e-05 TAATTTGTGA GTGGTCGCACAT ATCCTGTT  
ilv                          -     39  7.25e-05 AATTGAGGGG TTGATCACGTTT TGTACTGAAT
gale                         +     52  7.25e-05 TAATTTATTC CATGTCACACTT TTCGCATCTT
cya                          +     60  7.25e-05 AGGTGTTAAA TTGATCACGTTT TAGACCATTT
malk                         -     29  8.14e-05 GACCTCGGTT TAGTTCACAGAA GCCGTGTTCT
bglr1                        -     76  2.67e-04 AAATATGACC ATGCTCACAGTT ATTAACTTTG
trn9cat                      +     15  3.73e-04 GACGGAAGAT CACTTCGCAGAA TAAATAAATC
lac                          -      9  3.73e-04 ATGAGTGAGC TAACTCACATTA ATTGCGTT  
uxu1                         -     81  5.75e-04 TGCATCGGAT GAGATGGCGTAT AAGTTCTACC
pbr322                       +     63  6.90e-04 CGGTGTGAAA TACCGCACAGAT GCGTAAGGAG
malt                         -     75  6.90e-04 TCTAATGCAA GCGATGACGTTT TTTTATGTGT
ce1cg                        +     71  7.81e-04 TTTTTTGATC GTTTTCACAAAA ATGGAAGTCC
tnaa                         -     71  1.68e-03 AAATGTGAAT CGAATCACAATC GTTCGGGGAG
--------------------------------------------------------------------------------

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	Motif BWSDTCACANWW MEME-2 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
ompa                                7e-07  57_[+2]_36
male                              4.2e-06  23_[+2]_70
crp                               1.3e-05  72_[+2]_21
ara                                 2e-05  64_[+2]_29
deop2                             3.4e-05  59_[-2]_34
tdc                               5.5e-05  85_[+2]_8
ilv                               7.2e-05  38_[-2]_55
gale                              7.2e-05  51_[+2]_42
cya                               7.2e-05  59_[+2]_34
malk                              8.1e-05  28_[-2]_65
bglr1                             0.00027  75_[-2]_18
trn9cat                           0.00037  14_[+2]_79
lac                               0.00037  8_[-2]_85
uxu1                              0.00058  80_[-2]_13
pbr322                            0.00069  62_[+2]_31
malt                              0.00069  74_[-2]_19
ce1cg                             0.00078  70_[+2]_23
tnaa                               0.0017  70_[-2]_23
--------------------------------------------------------------------------------

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	Motif BWSDTCACANWW MEME-2 in BLOCKS format
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BL   MOTIF BWSDTCACANWW width=12 seqs=18
ompa                     (   58) GAGTTCACACTT  1 
male                     (   24) GAGATCACACAA  1 
crp                      (   73) GACGTCACATTA  1 
ara                      (   65) GGCGTCACACTT  1 
deop2                    (   60) CACATCACAATT  1 
tdc                      (   86) GTGGTCGCACAT  1 
ilv                      (   39) TTGATCACGTTT  1 
gale                     (   52) CATGTCACACTT  1 
cya                      (   60) TTGATCACGTTT  1 
malk                     (   29) TAGTTCACAGAA  1 
bglr1                    (   76) ATGCTCACAGTT  1 
trn9cat                  (   15) CACTTCGCAGAA  1 
lac                      (    9) TAACTCACATTA  1 
uxu1                     (   81) GAGATGGCGTAT  1 
pbr322                   (   63) TACCGCACAGAT  1 
malt                     (   75) GCGATGACGTTT  1 
ce1cg                    (   71) GTTTTCACAAAA  1 
tnaa                     (   71) CGAATCACAATC  1 
//

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	Motif BWSDTCACANWW MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 2444 bayes= 6.53916 E= 1.4e-001 
  -245     18    118    -13 
    87   -182    -82    -13 
  -145     50    135   -145 
    35    -23     18    -45 
 -1081  -1081   -182    163 
 -1081    218    -82  -1081 
   145  -1081    -23  -1081 
 -1081    235  -1081  -1081 
   135  -1081     18  -1081 
   -87     50     18     13 
    35  -1081  -1081    101 
    13   -182  -1081    101 
--------------------------------------------------------------------------------

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	Motif BWSDTCACANWW MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 1.4e-001 
 0.055556  0.222222  0.444444  0.277778 
 0.555556  0.055556  0.111111  0.277778 
 0.111111  0.277778  0.500000  0.111111 
 0.388889  0.166667  0.222222  0.222222 
 0.000000  0.000000  0.055556  0.944444 
 0.000000  0.888889  0.111111  0.000000 
 0.833333  0.000000  0.166667  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.777778  0.000000  0.222222  0.000000 
 0.166667  0.277778  0.222222  0.333333 
 0.388889  0.000000  0.000000  0.611111 
 0.333333  0.055556  0.000000  0.611111 
--------------------------------------------------------------------------------

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	Motif BWSDTCACANWW MEME-2 regular expression
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[GTC][AT][GC][AGT]TCAC[AG][TCG][TA][TA]
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Time  0.41 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                            1.03e-02  18_[+1(5.30e-05)]_75
ara                              7.33e-04  39_[-1(9.82e-05)]_13_[+2(2.02e-05)]_\
    29
bglr1                            8.90e-04  56_[-1(9.34e-06)]_37
crp                              1.18e-03  72_[+2(1.27e-05)]_21
cya                              9.90e-04  [-1(3.81e-05)]_47_[+2(7.25e-05)]_34
deop2                            1.16e-03  16_[+2(8.14e-05)]_31_[-2(3.38e-05)]_\
    34
gale                             6.56e-04  31_[-1(2.42e-05)]_8_[+2(7.25e-05)]_\
    42
ilv                              1.11e-02  38_[-2(7.25e-05)]_55
lac                              1.05e-05  74_[+1(6.94e-08)]_19
male                             6.10e-04  23_[+2(4.18e-06)]_70
malk                             2.83e-02  28_[-2(8.14e-05)]_65
malt                             4.44e-02  105
ompa                             9.72e-05  57_[+2(7.03e-07)]_36
tnaa                             1.33e-02  105
uxu1                             1.15e-02  7_[+1(8.05e-05)]_86
pbr322                           2.02e-02  105
trn9cat                          1.81e-02  105
tdc                              2.35e-03  85_[+2(5.55e-05)]_8
--------------------------------------------------------------------------------

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

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