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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 -minsites 3 -maxsites 17 common/crp0.s -oc results/meme2 -mod zoops -dna -revcomp -nmotifs 2 -objfun classic -minw 8 -nostatus 

model:  mod=         zoops    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=        3    maxsites=       17    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 AWDTGTGANVTNGNTCACA MEME-1	width =  19  sites =  17  llr = 183  E-value = 1.8e-007
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	Motif AWDTGTGANVTNGNTCACA MEME-1 Description
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Simplified        A  7521:1:8221224:1827
pos.-specific     C  ::11:::1222412:8:61
probability       G  :13:a:9135:2521:212
matrix            T  3449:91:21632392:1:

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

Multilevel           AATTGTGAGGTCGATCACA
consensus            TTG     AACT T  GA 
sequence               A     CC         
                             T          
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	Motif AWDTGTGANVTNGNTCACA MEME-1 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                   Site      
-------------            ------  ----- ---------            -------------------
ara                          -     58  1.40e-07 TGGCATAGCA AAGTGTGACGCCGTGCAAA TAATCAATGT
deop2                        +     60  8.95e-07 AGATTTCCTT AATTGTGATGTGTATCGAA GTGTGTTGCG
pbr322                       -     56  1.53e-06 CTCCTTACGC ATCTGTGCGGTATTTCACA CCGCATATGG
ompa                         -     51  1.53e-06 GAAAACTTAC AAGTGTGAACTCCGTCAGG CATATGAAAA
ilv                          -     42  1.88e-06 GCAAAGGGAA AATTGAGGGGTTGATCACG TTTTGTACTG
tdc                          -     81  2.30e-06     AACAGG ATATGTGCGACCACTCACA AATTAACTTT
crp                          -     66  2.30e-06 TACTGCACGG TAATGTGACGTCCTTTGCA TACATGCAGT
male                         -     17  2.79e-06 CACCGTCGCT TTGTGTGATCTCTGTTACA GAATTGGCGG
ce1cg                        -     64  2.79e-06 GGACTTCCAT TTTTGTGAAAACGATCAAA AAAACAGTCT
malt                         +     41  3.71e-06 AAAGATTTGG AATTGTGACACAGTGCAAA TTCAGACACA
tnaa                         -     74  4.45e-06 GAAATTGTTT AAATGTGAATCGAATCACA ATCGTTCGGG
lac                          -     12  4.45e-06 GGGGTGCCTA ATGAGTGAGCTAACTCACA TTAATTGCGT
bglr1                        +     76  5.32e-06 CAAAGTTAAT AACTGTGAGCATGGTCATA TTTTTATCAA
trn9cat                      +     84  7.52e-06 CTTTTGGCGA AAATGAGACGTTGATCGGC ACG       
cya                          +     50  1.04e-05 TCAATCAGCA AGGTGTTAAATTGATCACG TTTTAGACCA
malk                         +     61  1.32e-05 ATGTAAGGAA TTTCGTGATGTTGCTTGCA AAAATCGTGG
uxu1                         +     17  1.54e-05 AGAGTGAAAT TGTTGTGATGTGGTTAACC CAATTAGAAT
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	Motif AWDTGTGANVTNGNTCACA MEME-1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
ara                               1.4e-07  57_[-1]_29
deop2                             8.9e-07  59_[+1]_27
pbr322                            1.5e-06  55_[-1]_31
ompa                              1.5e-06  50_[-1]_36
ilv                               1.9e-06  41_[-1]_45
tdc                               2.3e-06  80_[-1]_6
crp                               2.3e-06  65_[-1]_21
male                              2.8e-06  16_[-1]_70
ce1cg                             2.8e-06  63_[-1]_23
malt                              3.7e-06  40_[+1]_46
tnaa                              4.5e-06  73_[-1]_13
lac                               4.5e-06  11_[-1]_75
bglr1                             5.3e-06  75_[+1]_11
trn9cat                           7.5e-06  83_[+1]_3
cya                                 1e-05  49_[+1]_37
malk                              1.3e-05  60_[+1]_26
uxu1                              1.5e-05  16_[+1]_70
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	Motif AWDTGTGANVTNGNTCACA MEME-1 in BLOCKS format
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BL   MOTIF AWDTGTGANVTNGNTCACA width=19 seqs=17
ara                      (   58) AAGTGTGACGCCGTGCAAA  1 
deop2                    (   60) AATTGTGATGTGTATCGAA  1 
pbr322                   (   56) ATCTGTGCGGTATTTCACA  1 
ompa                     (   51) AAGTGTGAACTCCGTCAGG  1 
ilv                      (   42) AATTGAGGGGTTGATCACG  1 
tdc                      (   81) ATATGTGCGACCACTCACA  1 
crp                      (   66) TAATGTGACGTCCTTTGCA  1 
male                     (   17) TTGTGTGATCTCTGTTACA  1 
ce1cg                    (   64) TTTTGTGAAAACGATCAAA  1 
malt                     (   41) AATTGTGACACAGTGCAAA  1 
tnaa                     (   74) AAATGTGAATCGAATCACA  1 
lac                      (   12) ATGAGTGAGCTAACTCACA  1 
bglr1                    (   76) AACTGTGAGCATGGTCATA  1 
trn9cat                  (   84) AAATGAGACGTTGATCGGC  1 
cya                      (   50) AGGTGTTAAATTGATCACG  1 
malk                     (   61) TTTCGTGATGTTGCTTGCA  1 
uxu1                     (   17) TGTTGTGATGTGGTTAACC  1 
//

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	Motif AWDTGTGANVTNGNTCACA MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 19 n= 1566 bayes= 6.9004 E= 1.8e-007 
   121  -1073  -1073     -5 
    80  -1073    -73     21 
   -37    -73     59     21 
  -237   -173  -1073    154 
 -1073  -1073    235  -1073 
  -137  -1073  -1073    154 
 -1073  -1073    226   -237 
   144    -73   -173  -1073 
   -37     26     59    -37 
   -37     26    126   -237 
  -137     26  -1073    109 
   -78     85    -15     -5 
   -78    -73    143    -78 
    21    -15    -15     -5 
 -1073  -1073    -73    154 
  -237    196  -1073    -78 
   133  -1073     26  -1073 
   -37    159    -73   -237 
   121    -73    -15  -1073 
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	Motif AWDTGTGANVTNGNTCACA MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 19 nsites= 17 E= 1.8e-007 
 0.705882  0.000000  0.000000  0.294118 
 0.529412  0.000000  0.117647  0.352941 
 0.235294  0.117647  0.294118  0.352941 
 0.058824  0.058824  0.000000  0.882353 
 0.000000  0.000000  1.000000  0.000000 
 0.117647  0.000000  0.000000  0.882353 
 0.000000  0.000000  0.941176  0.058824 
 0.823529  0.117647  0.058824  0.000000 
 0.235294  0.235294  0.294118  0.235294 
 0.235294  0.235294  0.470588  0.058824 
 0.117647  0.235294  0.000000  0.647059 
 0.176471  0.352941  0.176471  0.294118 
 0.176471  0.117647  0.529412  0.176471 
 0.352941  0.176471  0.176471  0.294118 
 0.000000  0.000000  0.117647  0.882353 
 0.058824  0.764706  0.000000  0.176471 
 0.764706  0.000000  0.235294  0.000000 
 0.235294  0.588235  0.117647  0.058824 
 0.705882  0.117647  0.176471  0.000000 
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	Motif AWDTGTGANVTNGNTCACA MEME-1 regular expression
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[AT][AT][TGA]TGTGA[GACT][GAC][TC][CT]G[AT]TC[AG][CA]A
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Time  0.42 secs.

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MOTIF ASGRGSMRGRAGSAT MEME-2	width =  15  sites =   3  llr = 53  E-value = 2.5e+004
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	Motif ASGRGSMRGRAGSAT MEME-2 Description
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Simplified        A  a::7::33:3a::a:
pos.-specific     C  :3:::77:::::3::
probability       G  :7a3a3:7a7:a7::
matrix            T  ::::::::::::::a

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

Multilevel           AGGAGCCGGGAGGAT
consensus             C G GAA A  C  
sequence                            
                                    
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	Motif ASGRGSMRGRAGSAT MEME-2 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
malk                         +      3  1.01e-09         GG AGGAGGCGGGAGGAT GAGAACACGG
male                         +     52  1.51e-08 GGTGGGGCGT AGGGGCAAGGAGGAT GGAAAGAGGT
lac                          -     55  1.51e-08 CACACAACAT ACGAGCCGGAAGCAT AAAGTGTAAA
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	Motif ASGRGSMRGRAGSAT MEME-2 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
malk                                1e-09  2_[+2]_88
male                              1.5e-08  51_[+2]_39
lac                               1.5e-08  54_[-2]_36
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	Motif ASGRGSMRGRAGSAT MEME-2 in BLOCKS format
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BL   MOTIF ASGRGSMRGRAGSAT width=15 seqs=3
malk                     (    3) AGGAGGCGGGAGGAT  1 
male                     (   52) AGGGGCAAGGAGGAT  1 
lac                      (   55) ACGAGCCGGAAGCAT  1 
//

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	Motif ASGRGSMRGRAGSAT MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 15 n= 1638 bayes= 9.09011 E= 2.5e+004 
   171   -823   -823   -823 
  -823     77    176   -823 
  -823   -823    235   -823 
   113   -823     77   -823 
  -823   -823    235   -823 
  -823    176     77   -823 
    13    176   -823   -823 
    13   -823    176   -823 
  -823   -823    235   -823 
    13   -823    176   -823 
   171   -823   -823   -823 
  -823   -823    235   -823 
  -823     77    176   -823 
   171   -823   -823   -823 
  -823   -823   -823    171 
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	Motif ASGRGSMRGRAGSAT MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 15 nsites= 3 E= 2.5e+004 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.333333  0.666667  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.666667  0.000000  0.333333  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.666667  0.333333  0.000000 
 0.333333  0.666667  0.000000  0.000000 
 0.333333  0.000000  0.666667  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.333333  0.000000  0.666667  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.333333  0.666667  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

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	Motif ASGRGSMRGRAGSAT MEME-2 regular expression
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A[GC]G[AG]G[CG][CA][GA]G[GA]AG[GC]AT
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Time  0.73 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                            3.97e-03  16_[+1(5.92e-05)]_28_[-1(2.79e-06)]_\
    23
ara                              2.80e-04  57_[-1(1.40e-07)]_29
bglr1                            3.50e-03  75_[+1(5.32e-06)]_11
crp                              1.65e-03  65_[-1(2.30e-06)]_21
cya                              4.05e-03  49_[+1(1.04e-05)]_37
deop2                            1.29e-03  59_[+1(8.95e-07)]_27
gale                             4.31e-02  26_[-1(4.35e-05)]_60
ilv                              2.90e-03  41_[-1(1.88e-06)]_45
lac                              4.47e-08  11_[-1(4.45e-06)]_24_[-2(1.51e-08)]_\
    36
male                             2.86e-08  16_[-1(2.79e-06)]_16_[+2(1.51e-08)]_\
    39
malk                             9.54e-09  2_[+2(1.01e-09)]_43_[+1(1.32e-05)]_\
    26
malt                             5.29e-03  40_[+1(3.71e-06)]_46
ompa                             2.03e-03  50_[-1(1.53e-06)]_36
tnaa                             2.44e-03  73_[-1(4.45e-06)]_13
uxu1                             1.80e-02  16_[+1(1.54e-05)]_70
pbr322                           1.08e-03  55_[-1(1.53e-06)]_31
trn9cat                          4.49e-03  83_[+1(7.52e-06)]_3
tdc                              3.42e-03  80_[-1(2.30e-06)]_6
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Stopped because requested number of motifs (2) found.
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CPU: Timothys-iMac.local

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