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MEME - Motif discovery tool
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MEME version 5.5.5 (Release date: Thu Sep 14 08:48:04 2023 +1000)

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/meme30 -mod anr -dna -revcomp -nmotifs 2 -objfun se -w 12 -hsfrac 0.6 -shuf 2 -nostatus 

model:  mod=           anr    nmotifs=         2    evt=           inf
objective function:           em=       Selective 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=        0.6
        searchsize=   1890    norand=         no    csites=         -1
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 CAVATCACAWWW MEME-1	width =  12  sites =  11  llr = 98  p-value = 4.6e-001  E-value = 4.6e-001
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	Motif CAVATCACAWWW MEME-1 Description
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Simplified        A  17471:6:9545
pos.-specific     C  72431a2a:2::
probability       G  113:::2:1:::
matrix            T  1:::8::::365

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

Multilevel           CAAATCACAATA
consensus              CC     TAT
sequence               G         
                                 
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	Motif CAVATCACAWWW MEME-1 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                Site  
-------------            ------  ----- ---------            ------------
deop2                        -     60  2.15e-07 CACTTCGATA CACATCACAATT AAGGAAATCT
bglr1                        -     21  4.69e-06 TTATATATAA CAAATCCCAATA ATTAAGTTAT
bglr1                        +      2  4.69e-06          A CAAATCCCAATA ACTTAATTAT
deop2                        +     17  9.63e-06 TTATTTGAAC CAGATCGCATTA CAGTGATGCA
lac                          -     81  1.06e-05 AAATTGTTAT CCGCTCACAATT CCACACAACA
tdc                          -     78  2.47e-05 ATATGTGCGA CCACTCACAAAT TAACTTTCAA
male                         +     24  6.47e-05 TTCTGTAACA GAGATCACACAA AGCGACGGTG
pbr322                       -     48  1.00e-04 TGCGGTATTT CACACCGCATAT GGTGCACTCT
lac                          -      9  1.00e-04 ATGAGTGAGC TAACTCACATTA ATTGCGTT  
deop2                        -     77  1.56e-04 ACATCTACTC CGCAACACACTT CGATACACAT
malk                         -     61  1.83e-04 TTTTGCAAGC AACATCACGAAA TTCCTTACAT
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	Motif CAVATCACAWWW MEME-1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
deop2                             0.00016  16_[+1]_31_[-1]_5_[-1]_17
bglr1                             4.7e-06  1_[+1]_7_[-1]_73
lac                                0.0001  8_[-1]_60_[-1]_13
tdc                               2.5e-05  77_[-1]_16
male                              6.5e-05  23_[+1]_70
pbr322                             0.0001  47_[-1]_46
malk                              0.00018  60_[-1]_33
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	Motif CAVATCACAWWW MEME-1 in BLOCKS format
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BL   MOTIF CAVATCACAWWW width=12 seqs=11
deop2                    (   60) CACATCACAATT  1 
bglr1                    (   21) CAAATCCCAATA  1 
bglr1                    (    2) CAAATCCCAATA  1 
deop2                    (   17) CAGATCGCATTA  1 
lac                      (   81) CCGCTCACAATT  1 
tdc                      (   78) CCACTCACAAAT  1 
male                     (   24) GAGATCACACAA  1 
pbr322                   (   48) CACACCGCATAT  1 
lac                      (    9) TAACTCACATTA  1 
deop2                    (   77) CGCAACACACTT  1 
malk                     (   61) AACATCACGAAA  1 
//

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	Motif CAVATCACAWWW MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 7.36529 E= 4.6e-001 
  -174    189   -111   -174 
   126    -11   -111  -1010 
    26     89     48  -1010 
   126     48  -1010  -1010 
  -174   -111  -1010    143 
 -1010    235  -1010  -1010 
   106    -11    -11  -1010 
 -1010    235  -1010  -1010 
   158  -1010   -111  -1010 
    84    -11  -1010    -16 
    26  -1010  -1010    106 
    84  -1010  -1010     58 
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	Motif CAVATCACAWWW MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 11 E= 4.6e-001 
 0.090909  0.727273  0.090909  0.090909 
 0.727273  0.181818  0.090909  0.000000 
 0.363636  0.363636  0.272727  0.000000 
 0.727273  0.272727  0.000000  0.000000 
 0.090909  0.090909  0.000000  0.818182 
 0.000000  1.000000  0.000000  0.000000 
 0.636364  0.181818  0.181818  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.909091  0.000000  0.090909  0.000000 
 0.545455  0.181818  0.000000  0.272727 
 0.363636  0.000000  0.000000  0.636364 
 0.545455  0.000000  0.000000  0.454545 
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	Motif CAVATCACAWWW MEME-1 regular expression
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CA[ACG][AC]TCACA[AT][TA][AT]
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Time  0.25 secs.

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MOTIF ABSCSKAAKSAK MEME-2	width =  12  sites =  12  llr = 97  p-value = 3.2e-001  E-value = 3.2e-001
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	Motif ABSCSKAAKSAK MEME-2 Description
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Simplified        A  8:::::68::8:
pos.-specific     C  :3484221:331
probability       G  3363553:56:6
matrix            T  :4::13:151:3

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

Multilevel           ATGCGGAAGGAG
consensus            GCCGCTG TCCT
sequence              G          
                                 
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	Motif ABSCSKAAKSAK MEME-2 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                Site  
-------------            ------  ----- ---------            ------------
pbr322                       +     73  1.34e-06 TACCGCACAG ATGCGTAAGGAG AAAATACCGC
malk                         +      6  6.50e-06      GGAGG AGGCGGGAGGAT GAGAACACGG
pbr322                       +     12  1.20e-05 TGGCTTAACT ATGCGGCATCAG AGCAGATTGT
lac                          -     55  1.58e-05 ACAACATACG AGCCGGAAGCAT AAAGTGTAAA
lac                          -     26  1.82e-05 AAAGCCTGGG GTGCCTAATGAG TGAGCTAACT
male                         +     52  2.34e-05 GGTGGGGCGT AGGGGCAAGGAG GATGGAAAGA
pbr322                       -     92  6.11e-05         GA GCGCCTGATGCG GTATTTTCTC
ilv                          -      2  6.11e-05 ATAACAAAAA ACCCCGCCGGAG C         
trn9cat                      +     54  2.28e-04 CCCTGTTGAT ACCGGGAAGCCC TGGGCCAACT
uxu1                         -     41  3.26e-04 AGACATGTCA ATCCCGAATTCT AATTGGGTTA
cya                          +     36  3.83e-04 ATCTTTCTTT ACGGTCAATCAG CAAGGTGTTA
trn9cat                      +     42  6.29e-04 AAATCCTGGT GTCCCTGTTGAT ACCGGGAAGC
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	Motif ABSCSKAAKSAK MEME-2 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
pbr322                            6.1e-05  11_[+2]_49_[+2]_7_[-2]_2
malk                              6.5e-06  5_[+2]_88
lac                               1.6e-05  25_[-2]_17_[-2]_39
male                              2.3e-05  51_[+2]_42
ilv                               6.1e-05  1_[-2]_92
trn9cat                           0.00023  41_[+2]_[+2]_40
uxu1                              0.00033  40_[-2]_53
cya                               0.00038  35_[+2]_58
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	Motif ABSCSKAAKSAK MEME-2 in BLOCKS format
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BL   MOTIF ABSCSKAAKSAK width=12 seqs=12
pbr322                   (   73) ATGCGTAAGGAG  1 
malk                     (    6) AGGCGGGAGGAT  1 
pbr322                   (   12) ATGCGGCATCAG  1 
lac                      (   55) AGCCGGAAGCAT  1 
lac                      (   26) GTGCCTAATGAG  1 
male                     (   52) AGGGGCAAGGAG  1 
pbr322                   (   92) GCGCCTGATGCG  1 
ilv                      (    2) ACCCCGCCGGAG  1 
trn9cat                  (   54) ACCGGGAAGCCC  1 
uxu1                     (   41) ATCCCGAATTCT  1 
cya                      (   36) ACGGTCAATCAG  1 
trn9cat                  (   42) GTCCCTGTTGAT  1 
//

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	Motif ABSCSKAAKSAK MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 7.71768 E= 3.2e-001 
   130  -1023     35  -1023 
 -1023     77     35     45 
 -1023    109    157  -1023 
 -1023    194     35  -1023 
 -1023    109    135   -186 
 -1023    -23    135     13 
    94    -23     35  -1023 
   145   -123  -1023   -186 
 -1023  -1023    135     72 
 -1023     77    157   -186 
   130     35  -1023  -1023 
 -1023   -123    157     13 
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	Motif ABSCSKAAKSAK MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 12 E= 3.2e-001 
 0.750000  0.000000  0.250000  0.000000 
 0.000000  0.333333  0.250000  0.416667 
 0.000000  0.416667  0.583333  0.000000 
 0.000000  0.750000  0.250000  0.000000 
 0.000000  0.416667  0.500000  0.083333 
 0.000000  0.166667  0.500000  0.333333 
 0.583333  0.166667  0.250000  0.000000 
 0.833333  0.083333  0.000000  0.083333 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  0.333333  0.583333  0.083333 
 0.750000  0.250000  0.000000  0.000000 
 0.000000  0.083333  0.583333  0.333333 
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	Motif ABSCSKAAKSAK MEME-2 regular expression
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[AG][TCG][GC][CG][GC][GT][AG]A[GT][GC][AC][GT]
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Time  0.46 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                            1.56e-01  105
ara                              3.21e-01  105
bglr1                            6.98e-03  1_[+1(4.69e-06)]_7_[-1(4.69e-06)]_\
    73
crp                              1.71e-01  105
cya                              1.50e-01  105
deop2                            2.93e-04  16_[+1(9.63e-06)]_31_[-1(2.15e-07)]_\
    34
gale                             8.81e-01  105
ilv                              1.19e-02  1_[-2(6.11e-05)]_92
lac                              7.71e-05  8_[-1(1.00e-04)]_5_[-2(1.82e-05)]_\
    17_[-2(1.58e-05)]_14_[-1(1.06e-05)]_13
male                             5.76e-04  23_[+1(6.47e-05)]_16_[+2(2.34e-05)]_\
    42
malk                             4.58e-04  5_[+2(6.50e-06)]_88
malt                             4.68e-01  105
ompa                             3.65e-01  105
tnaa                             4.13e-01  105
uxu1                             3.47e-02  105
pbr322                           6.23e-05  11_[+2(1.20e-05)]_24_[-1(1.00e-04)]_\
    13_[+2(1.34e-06)]_7_[-2(6.11e-05)]_2
trn9cat                          1.28e-01  105
tdc                              2.62e-02  77_[-1(2.47e-05)]_16
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Stopped because requested number of motifs (2) found.
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CPU: Timothys-iMac.local

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