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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 -minsites 3 -maxsites 17 common/crp0.s -oc results/meme29 -mod zoops -dna -revcomp -nmotifs 2 -objfun se -w 12 -hsfrac 0.6 -shuf 2 -nostatus -mpi 

model:  mod=         zoops    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 TGKRMGGWAWTG MEME-1	width =  12  sites =  10  llr = 93  p-value = 1.1e-001  E-value = 1.1e-001
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	Motif TGKRMGGWAWTG MEME-1 Description
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Simplified        A  :::53116a3::
pos.-specific     C  ::1:51::::::
probability       G  :734:79::1:7
matrix            T  a36121:4:6a3

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

Multilevel           TGTACGGAATTG
consensus             TGGA  T A T
sequence                 T       
                                 
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	Motif TGKRMGGWAWTG MEME-1 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                Site  
-------------            ------  ----- ---------            ------------
lac                          +     74  1.33e-06 GCTCGTATGT TGTGTGGAATTG TGAGCGGATA
pbr322                       -     60  2.44e-06 CTTACGCATC TGTGCGGTATTT CACACCGCAT
malk                         +     52  6.19e-06 ACCGAGGTCA TGTAAGGAATTT CGTGATGTTG
ilv                          -     27  7.46e-06 GATCACGTTT TGTACTGAATTG CAGATAACAA
male                         -      2  8.76e-06 TGTTACAGAA TTGGCGGTAATG T         
crp                          -     80  8.76e-06 TCAACTGTAC TGCACGGTAATG TGACGTCCTT
tdc                          +     59  4.42e-05 AACGATACTC TGGAAAGTATTG AAAGTTAATT
trn9cat                      +     77  7.60e-05 GGGCCAACTT TTGGCGAAAATG AGACGTTGAT
deop2                        +     70  7.60e-05 AATTGTGATG TGTATCGAAGTG TGTTGCGGAG
bglr1                        -     49  1.04e-04 CTTTGTGTAA TTTTAGGAATTT ATAAAGTTAT
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	Motif TGKRMGGWAWTG MEME-1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
lac                               1.3e-06  73_[+1]_20
pbr322                            2.4e-06  59_[-1]_34
malk                              6.2e-06  51_[+1]_42
ilv                               7.5e-06  26_[-1]_67
male                              8.8e-06  1_[-1]_92
crp                               8.8e-06  79_[-1]_14
tdc                               4.4e-05  58_[+1]_35
trn9cat                           7.6e-05  76_[+1]_17
deop2                             7.6e-05  69_[+1]_24
bglr1                              0.0001  48_[-1]_45
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	Motif TGKRMGGWAWTG MEME-1 in BLOCKS format
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BL   MOTIF TGKRMGGWAWTG width=12 seqs=10
lac                      (   74) TGTGTGGAATTG  1 
pbr322                   (   60) TGTGCGGTATTT  1 
malk                     (   52) TGTAAGGAATTT  1 
ilv                      (   27) TGTACTGAATTG  1 
male                     (    2) TTGGCGGTAATG  1 
crp                      (   80) TGCACGGTAATG  1 
tdc                      (   59) TGGAAAGTATTG  1 
trn9cat                  (   77) TTGGCGAAAATG  1 
deop2                    (   70) TGTATCGAAGTG  1 
bglr1                    (   49) TTTTAGGAATTT  1 
//

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	Motif TGKRMGGWAWTG MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 7.95317 E= 1.1e-001 
  -997   -997   -997    172 
  -997   -997    184     -2 
  -997    -97     61     98 
    72   -997    103   -160 
    -2    135   -997    -60 
  -160    -97    184   -160 
  -160   -997    220   -997 
    98   -997   -997     40 
   172   -997   -997   -997 
    -2   -997    -97     98 
  -997   -997   -997    172 
  -997   -997    184     -2 
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	Motif TGKRMGGWAWTG MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 10 E= 1.1e-001 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.700000  0.300000 
 0.000000  0.100000  0.300000  0.600000 
 0.500000  0.000000  0.400000  0.100000 
 0.300000  0.500000  0.000000  0.200000 
 0.100000  0.100000  0.700000  0.100000 
 0.100000  0.000000  0.900000  0.000000 
 0.600000  0.000000  0.000000  0.400000 
 1.000000  0.000000  0.000000  0.000000 
 0.300000  0.000000  0.100000  0.600000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.700000  0.300000 
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	Motif TGKRMGGWAWTG MEME-1 regular expression
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T[GT][TG][AG][CAT]GG[AT]A[TA]T[GT]
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Time  0.20 secs.

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MOTIF AKKYGKAAGKAG MEME-2	width =  12  sites =   7  llr = 65  p-value = 6.8e-001  E-value = 6.8e-001
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	Motif AKKYGKAAGKAG MEME-2 Description
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Simplified        A  9:::::7a::7:
pos.-specific     C  :1:411::::::
probability       G  1361933:7637
matrix            T  :644:6::34:3

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

Multilevel           ATGCGTAAGGAG
consensus             GTT GG TTGT
sequence                         
                                 
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	Motif AKKYGKAAGKAG MEME-2 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                Site  
-------------            ------  ----- ---------            ------------
pbr322                       +     73  4.47e-08 TACCGCACAG ATGCGTAAGGAG AAAATACCGC
male                         +     52  8.77e-06 GGTGGGGCGT AGGGGCAAGGAG GATGGAAAGA
malk                         +      6  1.14e-05      GGAGG AGGCGGGAGGAT GAGAACACGG
deop2                        +     40  1.97e-05 AGTGATGCAA ACTTGTAAGTAG ATTTCCTTAA
tdc                          +     78  2.13e-05 TTGAAAGTTA ATTTGTGAGTGG TCGCACATAT
lac                          -     26  9.09e-05 AAAGCCTGGG GTGCCTAATGAG TGAGCTAACT
malt                         +     35  1.51e-04 GTTAATAAAG ATTTGGAATTGT GACACAGTGC
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	Motif AKKYGKAAGKAG MEME-2 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
pbr322                            4.5e-08  72_[+2]_21
male                              8.8e-06  51_[+2]_42
malk                              1.1e-05  5_[+2]_88
deop2                               2e-05  39_[+2]_54
tdc                               2.1e-05  77_[+2]_16
lac                               9.1e-05  25_[-2]_68
malt                              0.00015  34_[+2]_59
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	Motif AKKYGKAAGKAG MEME-2 in BLOCKS format
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BL   MOTIF AKKYGKAAGKAG width=12 seqs=7
pbr322                   (   73) ATGCGTAAGGAG  1 
male                     (   52) AGGGGCAAGGAG  1 
malk                     (    6) AGGCGGGAGGAT  1 
deop2                    (   40) ACTTGTAAGTAG  1 
tdc                      (   78) ATTTGTGAGTGG  1 
lac                      (   26) GTGCCTAATGAG  1 
malt                     (   35) ATTTGGAATTGT  1 
//

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	Motif AKKYGKAAGKAG MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 8.28694 E= 6.8e-001 
   149   -945    -45   -945 
  -945    -45     54     91 
  -945   -945    154     49 
  -945    113    -45     49 
  -945    -45    213   -945 
  -945    -45     54     91 
   123   -945     54   -945 
   172   -945   -945   -945 
  -945   -945    187     -9 
  -945   -945    154     49 
   123   -945     54   -945 
  -945   -945    187     -9 
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	Motif AKKYGKAAGKAG MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 6.8e-001 
 0.857143  0.000000  0.142857  0.000000 
 0.000000  0.142857  0.285714  0.571429 
 0.000000  0.000000  0.571429  0.428571 
 0.000000  0.428571  0.142857  0.428571 
 0.000000  0.142857  0.857143  0.000000 
 0.000000  0.142857  0.285714  0.571429 
 0.714286  0.000000  0.285714  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.714286  0.285714 
 0.000000  0.000000  0.571429  0.428571 
 0.714286  0.000000  0.285714  0.000000 
 0.000000  0.000000  0.714286  0.285714 
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	Motif AKKYGKAAGKAG MEME-2 regular expression
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A[TG][GT][CT]G[TG][AG]A[GT][GT][AG][GT]
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Time  0.37 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                            1.65e-01  105
ara                              1.61e-01  105
bglr1                            4.97e-02  105
crp                              1.16e-02  79_[-1(8.76e-06)]_14
cya                              1.54e-01  105
deop2                            5.68e-04  39_[+2(1.97e-05)]_18_[+1(7.60e-05)]_\
    24
gale                             8.15e-01  105
ilv                              5.16e-03  26_[-1(7.46e-06)]_67
lac                              5.68e-05  25_[-2(9.09e-05)]_36_[+1(1.33e-06)]_\
    20
male                             3.74e-05  1_[-1(8.76e-06)]_38_[+2(8.77e-06)]_\
    42
malk                             3.47e-05  5_[+2(1.14e-05)]_34_[+1(6.19e-06)]_\
    42
malt                             7.31e-02  105
ompa                             4.14e-01  105
tnaa                             8.13e-01  105
uxu1                             3.71e-01  105
pbr322                           7.87e-08  59_[-1(2.44e-06)]_1_[+2(4.47e-08)]_\
    21
trn9cat                          7.23e-02  76_[+1(7.60e-05)]_17
tdc                              3.74e-04  58_[+1(4.42e-05)]_7_[+2(2.13e-05)]_\
    16
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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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