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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 3-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/meme20 -mod zoops -dna -revcomp -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus 

model:  mod=         zoops    nmotifs=         2    evt=           inf
objective function:           em=       Differential Enrichment 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 KGMGYDDKBTCA MEME-1	width =  12  sites =   7  llr = 64  p-value = 7.5e-001  E-value = 7.5e-001
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	Motif KGMGYDDKBTCA MEME-1 Description
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Simplified        A  ::6::33::::a
pos.-specific     C  114:3:::4:a:
probability       G  39:9134633::
matrix            T  6::1643437::

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

Multilevel           TGAGTTGGCTCA
consensus            G C CAATGG  
sequence                  GT T   
                                 
--------------------------------------------------------------------------------

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	Motif KGMGYDDKBTCA MEME-1 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                Site  
-------------            ------  ----- ---------            ------------
lac                          +     14  2.45e-06 GCAATTAATG TGAGTTAGCTCA CTCATTAGGC
tdc                          +     83  4.36e-06 AGTTAATTTG TGAGTGGTCGCA CATATCCTGT
male                         +     47  6.93e-06 GCGACGGTGG GGCGTAGGGGCA AGGAGGATGG
bglr1                        +     81  1.69e-05 TTAATAACTG TGAGCATGGTCA TATTTTTATC
pbr322                       -     58  6.55e-05 TACGCATCTG TGCGGTATTTCA CACCGCATAT
malk                         -     17  6.96e-05 GTTCACAGAA GCCGTGTTCTCA TCCTCCCGCC
deop2                        -     12  1.25e-04 CACTGTAATG CGATCTGGTTCA AATAATTCAC
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	Motif KGMGYDDKBTCA MEME-1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
lac                               2.4e-06  13_[+1]_80
tdc                               4.4e-06  82_[+1]_11
male                              6.9e-06  46_[+1]_47
bglr1                             1.7e-05  80_[+1]_13
pbr322                            6.5e-05  57_[-1]_36
malk                                7e-05  16_[-1]_77
deop2                             0.00012  11_[-1]_82
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	Motif KGMGYDDKBTCA MEME-1 in BLOCKS format
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BL   MOTIF KGMGYDDKBTCA width=12 seqs=7
lac                      (   14) TGAGTTAGCTCA  1 
tdc                      (   83) TGAGTGGTCGCA  1 
male                     (   47) GGCGTAGGGGCA  1 
bglr1                    (   81) TGAGCATGGTCA  1 
pbr322                   (   58) TGCGGTATTTCA  1 
malk                     (   17) GCCGTGTTCTCA  1 
deop2                    (   12) CGATCTGGTTCA  1 
//

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	Motif KGMGYDDKBTCA MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 7.91118 E= 7.5e-001 
  -945    -45     54     91 
  -945    -45    213   -945 
    91    113   -945   -945 
  -945   -945    213   -109 
  -945     54    -45     91 
    -9   -945     54     49 
    -9   -945    113     -9 
  -945   -945    154     49 
  -945    113     54     -9 
  -945   -945     54    123 
  -945    235   -945   -945 
   172   -945   -945   -945 
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	Motif KGMGYDDKBTCA MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 7.5e-001 
 0.000000  0.142857  0.285714  0.571429 
 0.000000  0.142857  0.857143  0.000000 
 0.571429  0.428571  0.000000  0.000000 
 0.000000  0.000000  0.857143  0.142857 
 0.000000  0.285714  0.142857  0.571429 
 0.285714  0.000000  0.285714  0.428571 
 0.285714  0.000000  0.428571  0.285714 
 0.000000  0.000000  0.571429  0.428571 
 0.000000  0.428571  0.285714  0.285714 
 0.000000  0.000000  0.285714  0.714286 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
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	Motif KGMGYDDKBTCA MEME-1 regular expression
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[TG]G[AC]G[TC][TAG][GAT][GT][CGT][TG]CA
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Time  0.24 secs.

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MOTIF TSTKTAAYTGTG MEME-2	width =  12  sites =   7  llr = 67  p-value = 9.9e-001  E-value = 9.9e-001
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	Motif TSTKTAAYTGTG MEME-2 Description
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Simplified        A  :1:::aa11113
pos.-specific     C  :33::::3::::
probability       G  16:41::::7:7
matrix            T  9:769::6919:

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

Multilevel           TGTTTAATTGTG
consensus             CCG   C   A
sequence                         
                                 
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	Motif TSTKTAAYTGTG MEME-2 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                Site  
-------------            ------  ----- ---------            ------------
deop2                        +     55  1.37e-06 TAAGTAGATT TCCTTAATTGTG ATGTGTATCG
lac                          +     76  1.68e-06 TCGTATGTTG TGTGGAATTGTG AGCGGATAAC
tnaa                         -     86  2.47e-06   TCTGAAAT TGTTTAAATGTG AATCGAATCA
tdc                          +     35  2.01e-05 TATTTAAAGG TATTTAATTGTA ATAACGATAC
bglr1                        -     56  2.27e-05 TTATTAACTT TGTGTAATTTTA GGAATTTATA
pbr322                       +      3  5.33e-05         CT GGCTTAACTATG CGGCATCAGA
male                         +     15  6.90e-05 TACCGCCAAT TCTGTAACAGAG ATCACACAAA
--------------------------------------------------------------------------------

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	Motif TSTKTAAYTGTG MEME-2 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
deop2                             1.4e-06  54_[+2]_39
lac                               1.7e-06  75_[+2]_18
tnaa                              2.5e-06  85_[-2]_8
tdc                                 2e-05  34_[+2]_59
bglr1                             2.3e-05  55_[-2]_38
pbr322                            5.3e-05  2_[+2]_91
male                              6.9e-05  14_[+2]_79
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	Motif TSTKTAAYTGTG MEME-2 in BLOCKS format
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BL   MOTIF TSTKTAAYTGTG width=12 seqs=7
deop2                    (   55) TCCTTAATTGTG  1 
lac                      (   76) TGTGGAATTGTG  1 
tnaa                     (   86) TGTTTAAATGTG  1 
tdc                      (   35) TATTTAATTGTA  1 
bglr1                    (   56) TGTGTAATTTTA  1 
pbr322                   (    3) GGCTTAACTATG  1 
male                     (   15) TCTGTAACAGAG  1 
//

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	Motif TSTKTAAYTGTG MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 8.08695 E= 9.9e-001 
  -945   -945    -45    149 
  -109     54    154   -945 
  -945     54   -945    123 
  -945   -945    113     91 
  -945   -945    -45    149 
   172   -945   -945   -945 
   172   -945   -945   -945 
  -109     54   -945     91 
  -109   -945   -945    149 
  -109   -945    187   -109 
  -109   -945   -945    149 
    -9   -945    187   -945 
--------------------------------------------------------------------------------

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	Motif TSTKTAAYTGTG MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 9.9e-001 
 0.000000  0.000000  0.142857  0.857143 
 0.142857  0.285714  0.571429  0.000000 
 0.000000  0.285714  0.000000  0.714286 
 0.000000  0.000000  0.428571  0.571429 
 0.000000  0.000000  0.142857  0.857143 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.142857  0.285714  0.000000  0.571429 
 0.142857  0.000000  0.000000  0.857143 
 0.142857  0.000000  0.714286  0.142857 
 0.142857  0.000000  0.000000  0.857143 
 0.285714  0.000000  0.714286  0.000000 
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	Motif TSTKTAAYTGTG MEME-2 regular expression
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T[GC][TC][TG]TAA[TC]TGT[GA]
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Time  0.45 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                            1.24e-01  105
ara                              8.12e-02  105
bglr1                            1.65e-04  55_[-2(2.27e-05)]_13_[+1(1.69e-05)]_\
    13
crp                              6.63e-01  105
cya                              5.28e-01  105
deop2                            7.78e-05  54_[+2(1.37e-06)]_39
gale                             8.11e-01  105
ilv                              4.41e-01  105
lac                              2.43e-06  13_[+1(2.45e-06)]_50_[+2(1.68e-06)]_\
    18
male                             2.01e-04  14_[+2(6.90e-05)]_20_[+1(6.93e-06)]_\
    47
malk                             6.51e-02  16_[-1(6.96e-05)]_77
malt                             3.99e-02  105
ompa                             4.17e-01  105
tnaa                             1.88e-03  85_[-2(2.47e-06)]_8
uxu1                             6.49e-01  105
pbr322                           1.22e-03  2_[+2(5.33e-05)]_43_[-1(6.55e-05)]_\
    36
trn9cat                          5.52e-01  105
tdc                              4.22e-05  34_[+2(2.01e-05)]_36_[+1(4.36e-06)]_\
    11
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Stopped because requested number of motifs (2) found.
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CPU: Timothys-iMac.local

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