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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 common/crp0.s -oc results/meme1 -mod oops -dna -revcomp -nmotifs 2 -objfun classic -minw 8 -nostatus 

model:  mod=          oops    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=       18    maxsites=       18    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 TGTGAMRTNGHTCAC MEME-1	width =  15  sites =  18  llr = 170  E-value = 9.6e-007
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	Motif TGTGAMRTNGHTCAC MEME-1 Description
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Simplified        A  :1119231314:172
pos.-specific     C  11:1:412213:8:7
probability       G  :9:8124227:2:31
matrix            T  9:91:22532381::

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

Multilevel           TGTGACGTTGATCAC
consensus                 AACA TG GA
sequence                     G C    
                                    
--------------------------------------------------------------------------------

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	Motif TGTGAMRTNGHTCAC MEME-1 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
lac                          +     12  5.04e-07 ACGCAATTAA TGTGAGTTAGCTCAC TCATTAGGCA
ara                          -     59  1.52e-06 CATAGCAAAG TGTGACGCCGTGCAA ATAATCAATG
malt                         +     44  3.31e-06 GATTTGGAAT TGTGACACAGTGCAA ATTCAGACAC
pbr322                       +     56  6.76e-06 CCATATGCGG TGTGAAATACCGCAC AGATGCGTAA
uxu1                         +     20  7.45e-06 GTGAAATTGT TGTGATGTGGTTAAC CCAATTAGAA
male                         +     17  9.01e-06 CCGCCAATTC TGTAACAGAGATCAC ACAAAGCGAC
cya                          +     53  1.09e-05 ATCAGCAAGG TGTTAAATTGATCAC GTTTTAGACC
trn9cat                      +     87  1.43e-05 TTGGCGAAAA TGAGACGTTGATCGG CACG      
deop2                        +     63  1.43e-05 TTTCCTTAAT TGTGATGTGTATCGA AGTGTGTTGC
crp                          -     67  1.43e-05 TGCACGGTAA TGTGACGTCCTTTGC ATACATGCAG
ce1cg                        -     65  1.43e-05 CTTCCATTTT TGTGAAAACGATCAA AAAAACAGTC
tdc                          +     81  1.85e-05 AAAGTTAATT TGTGAGTGGTCGCAC ATATCCTGTT
ompa                         +     51  1.85e-05 TTTTCATATG CCTGACGGAGTTCAC ACTTGTAAGT
ilv                          -     43  1.85e-05 AAGGGAAAAT TGAGGGGTTGATCAC GTTTTGTACT
tnaa                         -     75  2.20e-05 ATTGTTTAAA TGTGAATCGAATCAC AATCGTTCGG
malk                         +     64  2.59e-05 TAAGGAATTT CGTGATGTTGCTTGC AAAAATCGTG
gale                         +     54  3.88e-05 ATTTATTCCA TGTCACACTTTTCGC ATCTTTGTTA
bglr1                        -     80  5.71e-05 TTGATAAAAA TATGACCATGCTCAC AGTTATTAAC
--------------------------------------------------------------------------------

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	Motif TGTGAMRTNGHTCAC MEME-1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
lac                                 5e-07  11_[+1]_79
ara                               1.5e-06  58_[-1]_32
malt                              3.3e-06  43_[+1]_47
pbr322                            6.8e-06  55_[+1]_35
uxu1                              7.5e-06  19_[+1]_71
male                                9e-06  16_[+1]_74
cya                               1.1e-05  52_[+1]_38
trn9cat                           1.4e-05  86_[+1]_4
deop2                             1.4e-05  62_[+1]_28
crp                               1.4e-05  66_[-1]_24
ce1cg                             1.4e-05  64_[-1]_26
tdc                               1.9e-05  80_[+1]_10
ompa                              1.9e-05  50_[+1]_40
ilv                               1.9e-05  42_[-1]_48
tnaa                              2.2e-05  74_[-1]_16
malk                              2.6e-05  63_[+1]_27
gale                              3.9e-05  53_[+1]_37
bglr1                             5.7e-05  79_[-1]_11
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	Motif TGTGAMRTNGHTCAC MEME-1 in BLOCKS format
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BL   MOTIF TGTGAMRTNGHTCAC width=15 seqs=18
lac                      (   12) TGTGAGTTAGCTCAC  1 
ara                      (   59) TGTGACGCCGTGCAA  1 
malt                     (   44) TGTGACACAGTGCAA  1 
pbr322                   (   56) TGTGAAATACCGCAC  1 
uxu1                     (   20) TGTGATGTGGTTAAC  1 
male                     (   17) TGTAACAGAGATCAC  1 
cya                      (   53) TGTTAAATTGATCAC  1 
trn9cat                  (   87) TGAGACGTTGATCGG  1 
deop2                    (   63) TGTGATGTGTATCGA  1 
crp                      (   67) TGTGACGTCCTTTGC  1 
ce1cg                    (   65) TGTGAAAACGATCAA  1 
tdc                      (   81) TGTGAGTGGTCGCAC  1 
ompa                     (   51) CCTGACGGAGTTCAC  1 
ilv                      (   43) TGAGGGGTTGATCAC  1 
tnaa                     (   75) TGTGAATCGAATCAC  1 
malk                     (   64) CGTGATGTTGCTTGC  1 
gale                     (   54) TGTCACACTTTTCGC  1 
bglr1                    (   80) TATGACCATGCTCAC  1 
//

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	Motif TGTGAMRTNGHTCAC MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 15 n= 1638 bayes= 6.49185 E= 9.6e-007 
 -1081    -82  -1081    155 
  -245   -182    218  -1081 
  -145  -1081  -1081    155 
  -245   -182    209   -245 
   163  -1081   -182  -1081 
   -45    118    -23    -87 
    13   -182    118    -87 
  -145     18    -23     72 
   -13    -23     18     13 
  -245    -82    177    -87 
    35     50  -1081     13 
 -1081  -1081     18    135 
  -245    209  -1081   -145 
   125  -1081     50  -1081 
   -45    188   -182  -1081 
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	Motif TGTGAMRTNGHTCAC MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 15 nsites= 18 E= 9.6e-007 
 0.000000  0.111111  0.000000  0.888889 
 0.055556  0.055556  0.888889  0.000000 
 0.111111  0.000000  0.000000  0.888889 
 0.055556  0.055556  0.833333  0.055556 
 0.944444  0.000000  0.055556  0.000000 
 0.222222  0.444444  0.166667  0.166667 
 0.333333  0.055556  0.444444  0.166667 
 0.111111  0.222222  0.166667  0.500000 
 0.277778  0.166667  0.222222  0.333333 
 0.055556  0.111111  0.666667  0.166667 
 0.388889  0.277778  0.000000  0.333333 
 0.000000  0.000000  0.222222  0.777778 
 0.055556  0.833333  0.000000  0.111111 
 0.722222  0.000000  0.277778  0.000000 
 0.222222  0.722222  0.055556  0.000000 
--------------------------------------------------------------------------------

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	Motif TGTGAMRTNGHTCAC MEME-1 regular expression
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TGTGA[CA][GA][TC][TAG]G[ATC][TG]C[AG][CA]
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Time  0.35 secs.

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MOTIF CTTTACAR MEME-2	width =   8  sites =  18  llr = 109  E-value = 2.4e+008
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	Motif CTTTACAR MEME-2 Description
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Simplified        A  :2:28194
pos.-specific     C  a1:128:1
probability       G  :111::14
matrix            T  :697:1:2

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

Multilevel           CTTTACAA
consensus             A  C  G
sequence                     
                             
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	Motif CTTTACAR MEME-2 sites sorted by position p-value
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Sequence name            Strand  Start   P-value              Site
-------------            ------  ----- ---------            --------
ilv                          -     94  1.95e-05       ACAG CTTTACAG GGGAGACAAT
tdc                          -     58  6.25e-05 ACTTTCAATA CTTTCCAG AGTATCGTTA
deop2                        +     24  8.20e-05 AACCAGATCG CATTACAG TGATGCAAAC
ompa                         +     94  1.45e-04 ACGTTGTAGA CTTTACAT CGCC      
male                         -     65  3.29e-04 ACGGCAACCT CTTTCCAT CCTCCTTGCC
lac                          +     44  3.29e-04 GCACCCCAGG CTTTACAC TTTATGCTTC
ce1cg                        +     98  4.06e-04 AGTCCACAGT CTTGACAG           
cya                          +     32  5.39e-04 GCGCATCTTT CTTTACGG TCAATCAGCA
uxu1                         +     61  6.30e-04 ATTGACATGT CTTACCAA AAGGTAGAAC
crp                          +     90  6.30e-04 CATTACCGTG CAGTACAG TTGATAGC  
gale                         -     73  8.47e-04 ATAACCATAG CATAACAA AGATGCGAAA
bglr1                        +     43  8.47e-04 TTATATATAA CTTTATAA ATTCCTAAAA
pbr322                       -     30  9.49e-04 GGTGCACTCT CAGTACAA TCTGCTCTGA
ara                          +     11  1.05e-03 GACAAAAACG CGTAACAA AAGTGTCTAT
malk                         -     51  1.09e-03 TCACGAAATT CCTTACAT GACCTCGGTT
trn9cat                      -      1  1.30e-03 AGTGATCTTC CGTCACAG           
tnaa                         +     37  1.36e-03 AATTTATAAT CTTTAAAA AAAGCATTTA
malt                         -     92  1.50e-03     AGAAAC CTTTCTAA TGCAAGCGAT
--------------------------------------------------------------------------------

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	Motif CTTTACAR MEME-2 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
ilv                                 2e-05  93_[-2]_4
tdc                               6.2e-05  57_[-2]_40
deop2                             8.2e-05  23_[+2]_74
ompa                              0.00014  93_[+2]_4
male                              0.00033  64_[-2]_33
lac                               0.00033  43_[+2]_54
ce1cg                             0.00041  97_[+2]
cya                               0.00054  31_[+2]_66
uxu1                              0.00063  60_[+2]_37
crp                               0.00063  89_[+2]_8
gale                              0.00085  72_[-2]_25
bglr1                             0.00085  42_[+2]_55
pbr322                            0.00095  29_[-2]_68
ara                                 0.001  10_[+2]_87
malk                               0.0011  50_[-2]_47
trn9cat                            0.0013  [-2]_97
tnaa                               0.0014  36_[+2]_61
malt                               0.0015  91_[-2]_6
--------------------------------------------------------------------------------

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	Motif CTTTACAR MEME-2 in BLOCKS format
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BL   MOTIF CTTTACAR width=8 seqs=18
ilv                      (   94) CTTTACAG  1 
tdc                      (   58) CTTTCCAG  1 
deop2                    (   24) CATTACAG  1 
ompa                     (   94) CTTTACAT  1 
male                     (   65) CTTTCCAT  1 
lac                      (   44) CTTTACAC  1 
ce1cg                    (   98) CTTGACAG  1 
cya                      (   32) CTTTACGG  1 
uxu1                     (   61) CTTACCAA  1 
crp                      (   90) CAGTACAG  1 
gale                     (   73) CATAACAA  1 
bglr1                    (   43) CTTTATAA  1 
pbr322                   (   30) CAGTACAA  1 
ara                      (   11) CGTAACAA  1 
malk                     (   51) CCTTACAT  1 
trn9cat                  (    1) CGTCACAG  1 
tnaa                     (   37) CTTTAAAA  1 
malt                     (   92) CTTTCTAA  1 
//

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	Motif CTTTACAR MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 1764 bayes= 6.59991 E= 2.4e+008 
 -1081    235  -1081  -1081 
   -45   -182    -82    101 
 -1081  -1081    -82    155 
   -87   -182   -182    125 
   135     18  -1081  -1081 
  -245    209  -1081   -145 
   163  -1081   -182  -1081 
    35   -182     99    -87 
--------------------------------------------------------------------------------

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	Motif CTTTACAR MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 8 nsites= 18 E= 2.4e+008 
 0.000000  1.000000  0.000000  0.000000 
 0.222222  0.055556  0.111111  0.611111 
 0.000000  0.000000  0.111111  0.888889 
 0.166667  0.055556  0.055556  0.722222 
 0.777778  0.222222  0.000000  0.000000 
 0.055556  0.833333  0.000000  0.111111 
 0.944444  0.000000  0.055556  0.000000 
 0.388889  0.055556  0.388889  0.166667 
--------------------------------------------------------------------------------

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	Motif CTTTACAR MEME-2 regular expression
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C[TA]TT[AC]CA[AG]
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Time  0.60 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                            1.89e-03  64_[-1(1.43e-05)]_26
ara                              5.57e-04  58_[-1(1.52e-06)]_32
bglr1                            1.18e-02  79_[-1(5.71e-05)]_11
crp                              2.75e-03  66_[-1(1.43e-05)]_24
cya                              1.89e-03  52_[+1(1.09e-05)]_38
deop2                            4.59e-04  23_[+2(8.20e-05)]_31_[+1(1.43e-05)]_\
    28
gale                             8.44e-03  53_[+1(3.88e-05)]_37
ilv                              1.58e-04  42_[-1(1.85e-05)]_36_[-2(1.95e-05)]_\
    4
lac                              7.49e-05  11_[+1(5.04e-07)]_79
male                             1.04e-03  16_[+1(9.01e-06)]_74
malk                             7.26e-03  63_[+1(2.59e-05)]_27
malt                             1.50e-03  43_[+1(3.31e-06)]_47
ompa                             9.66e-04  50_[+1(1.85e-05)]_40
tnaa                             7.46e-03  74_[-1(2.20e-05)]_16
uxu1                             1.54e-03  19_[+1(7.45e-06)]_71
pbr322                           1.98e-03  55_[+1(6.76e-06)]_35
trn9cat                          4.92e-03  86_[+1(1.43e-05)]_4
tdc                              4.55e-04  57_[-2(6.25e-05)]_15_[+1(1.85e-05)]_\
    10
--------------------------------------------------------------------------------

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

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