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MEME - Motif discovery tool
********************************************************************************
MEME version 5.0.0 (Release date: Sat Oct 28 09:21:30 2017 -0700)

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme-suite.org .

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://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= 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 -dna -revcomp -nmotifs 3 crp0.s 

model:  mod=         zoops    nmotifs=         3    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=        2    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 TKTGANCNABNTCACAHWT MEME-1	width =  19  sites =  18  llr = 191  E-value = 4.3e-009
********************************************************************************
--------------------------------------------------------------------------------
	Motif TKTGANCNABNTCACAHWT MEME-1 Description
--------------------------------------------------------------------------------
Simplified        A  :1:28322613::9:8333
pos.-specific     C  112:1252:431a:a:31:
probability       G  16:7:2132331:::11::
matrix            T  838113222228:1:1367

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

Multilevel           TGTGAACGACATCACAATT
consensus             TCA TAAGGC     CAA
sequence                    C TG     T  
                            T           
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TKTGANCNABNTCACAHWT MEME-1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                   Site      
-------------            ------  ----- ---------            -------------------
ara                          +     58  7.97e-08 ACATTGATTA TTTGCACGGCGTCACACTT TGCTATGCCA
deop2                        -     60  3.33e-07 CGCAACACAC TTCGATACACATCACAATT AAGGAAATCT
pbr322                       +     56  1.14e-06 CCATATGCGG TGTGAAATACCGCACAGAT GCGTAAGGAG
crp                          +     66  1.27e-06 ACTGCATGTA TGCAAAGGACGTCACATTA CCGTGCAGTA
malt                         -     41  1.77e-06 TGTGTCTGAA TTTGCACTGTGTCACAATT CCAAATCTTT
male                         +     17  1.97e-06 CCGCCAATTC TGTAACAGAGATCACACAA AGCGACGGTG
tdc                          +     81  3.31e-06 AAAGTTAATT TGTGAGTGGTCGCACATAT CCTGTT    
tnaa                         +     74  4.02e-06 CCCGAACGAT TGTGATTCGATTCACATTT AAACAATTTC
ompa                         +     51  4.02e-06 TTTTCATATG CCTGACGGAGTTCACACTT GTAAGTTTTC
lac                          +     12  4.43e-06 ACGCAATTAA TGTGAGTTAGCTCACTCAT TAGGCACCCC
ce1cg                        +     64  4.87e-06 AGACTGTTTT TTTGATCGTTTTCACAAAA ATGGAAGTCC
bglr1                        -     76  5.35e-06 TTGATAAAAA TATGACCATGCTCACAGTT ATTAACTTTG
gale                         +     45  7.68e-06 ATTCCACTAA TTTATTCCATGTCACACTT TTCGCATCTT
ilv                          +     42  8.39e-06 CAGTACAAAA CGTGATCAACCCCTCAATT TTCCCTTTGC
trn9cat                      -     84  1.08e-05        CGT GCCGATCAACGTCTCATTT TCGCCAAAAG
malk                         -     61  1.18e-05 CCACGATTTT TGCAAGCAACATCACGAAA TTCCTTACAT
uxu1                         -     17  1.90e-05 ATTCTAATTG GGTTAACCACATCACAACA ATTTCACTCT
cya                          +     53  3.16e-05 ATCAGCAAGG TGTTAAATTGATCACGTTT TAGACCATTT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TKTGANCNABNTCACAHWT MEME-1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
ara                                 8e-08  57_[+1]_29
deop2                             3.3e-07  59_[-1]_27
pbr322                            1.1e-06  55_[+1]_31
crp                               1.3e-06  65_[+1]_21
malt                              1.8e-06  40_[-1]_46
male                                2e-06  16_[+1]_70
tdc                               3.3e-06  80_[+1]_6
tnaa                                4e-06  73_[+1]_13
ompa                                4e-06  50_[+1]_36
lac                               4.4e-06  11_[+1]_75
ce1cg                             4.9e-06  63_[+1]_23
bglr1                             5.3e-06  75_[-1]_11
gale                              7.7e-06  44_[+1]_42
ilv                               8.4e-06  41_[+1]_45
trn9cat                           1.1e-05  83_[-1]_3
malk                              1.2e-05  60_[-1]_26
uxu1                              1.9e-05  16_[-1]_70
cya                               3.2e-05  52_[+1]_34
--------------------------------------------------------------------------------

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	Motif TKTGANCNABNTCACAHWT MEME-1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF TKTGANCNABNTCACAHWT width=19 seqs=18
ara                      (   58) TTTGCACGGCGTCACACTT  1 
deop2                    (   60) TTCGATACACATCACAATT  1 
pbr322                   (   56) TGTGAAATACCGCACAGAT  1 
crp                      (   66) TGCAAAGGACGTCACATTA  1 
malt                     (   41) TTTGCACTGTGTCACAATT  1 
male                     (   17) TGTAACAGAGATCACACAA  1 
tdc                      (   81) TGTGAGTGGTCGCACATAT  1 
tnaa                     (   74) TGTGATTCGATTCACATTT  1 
ompa                     (   51) CCTGACGGAGTTCACACTT  1 
lac                      (   12) TGTGAGTTAGCTCACTCAT  1 
ce1cg                    (   64) TTTGATCGTTTTCACAAAA  1 
bglr1                    (   76) TATGACCATGCTCACAGTT  1 
gale                     (   45) TTTATTCCATGTCACACTT  1 
ilv                      (   42) CGTGATCAACCCCTCAATT  1 
trn9cat                  (   84) GCCGATCAACGTCTCATTT  1 
malk                     (   61) TGCAAGCAACATCACGAAA  1 
uxu1                     (   17) GGTTAACCACATCACAACA  1 
cya                      (   53) TGTTAAATTGATCACGTTT  1 
//

--------------------------------------------------------------------------------

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	Motif TKTGANCNABNTCACAHWT MEME-1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 19 n= 1566 bayes= 7.2817 E= 4.3e-009 
 -1081    -82    -82    135 
  -245    -82    150    -13 
 -1081     18  -1081    135 
   -45  -1081    177   -145 
   145    -82  -1081   -245 
    13    -23    -23     13 
   -45    135    -82    -87 
   -45     18     77    -45 
   101  -1081     18    -87 
  -245    118     50    -45 
   -13     50     50    -87 
 -1081   -182    -82    145 
 -1081    235  -1081  -1081 
   155  -1081  -1081   -145 
 -1081    235  -1081  -1081 
   145  -1081    -82   -245 
    13     50    -82    -13 
    13   -182  -1081    101 
   -13  -1081  -1081    125 
--------------------------------------------------------------------------------

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	Motif TKTGANCNABNTCACAHWT MEME-1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 19 nsites= 18 E= 4.3e-009 
 0.000000  0.111111  0.111111  0.777778 
 0.055556  0.111111  0.555556  0.277778 
 0.000000  0.222222  0.000000  0.777778 
 0.222222  0.000000  0.666667  0.111111 
 0.833333  0.111111  0.000000  0.055556 
 0.333333  0.166667  0.166667  0.333333 
 0.222222  0.500000  0.111111  0.166667 
 0.222222  0.222222  0.333333  0.222222 
 0.611111  0.000000  0.222222  0.166667 
 0.055556  0.444444  0.277778  0.222222 
 0.277778  0.277778  0.277778  0.166667 
 0.000000  0.055556  0.111111  0.833333 
 0.000000  1.000000  0.000000  0.000000 
 0.888889  0.000000  0.000000  0.111111 
 0.000000  1.000000  0.000000  0.000000 
 0.833333  0.000000  0.111111  0.055556 
 0.333333  0.277778  0.111111  0.277778 
 0.333333  0.055556  0.000000  0.611111 
 0.277778  0.000000  0.000000  0.722222 
--------------------------------------------------------------------------------

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	Motif TKTGANCNABNTCACAHWT MEME-1 regular expression
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T[GT][TC][GA]A[AT][CA][GACT][AG][CGT][ACG]TCACA[ACT][TA][TA]
--------------------------------------------------------------------------------




Time  0.38 secs.

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MOTIF CGGYGGGG MEME-2	width =   8  sites =   2  llr = 24  E-value = 1.5e+004
********************************************************************************
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	Motif CGGYGGGG MEME-2 Description
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Simplified        A  ::::::::
pos.-specific     C  a::5::::
probability       G  :aa:aaaa
matrix            T  :::5::::

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

Multilevel           CGGCGGGG
consensus               T    
sequence                     
                             
--------------------------------------------------------------------------------

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	Motif CGGYGGGG MEME-2 sites sorted by position p-value
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Sequence name            Strand  Start   P-value              Site
-------------            ------  ----- ---------            --------
ilv                          +      5  2.18e-06       GCTC CGGCGGGG TTTTTTGTTA
male                         +     41  5.56e-06 CACAAAGCGA CGGTGGGG CGTAGGGGCA
--------------------------------------------------------------------------------

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	Motif CGGYGGGG MEME-2 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
ilv                               2.2e-06  4_[+2]_93
male                              5.6e-06  40_[+2]_57
--------------------------------------------------------------------------------

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	Motif CGGYGGGG MEME-2 in BLOCKS format
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BL   MOTIF CGGYGGGG width=8 seqs=2
ilv                      (    5) CGGCGGGG  1 
male                     (   41) CGGTGGGG  1 
//

--------------------------------------------------------------------------------

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	Motif CGGYGGGG MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 1764 bayes= 9.783 E= 1.5e+004 
  -765    235   -765   -765 
  -765   -765    235   -765 
  -765   -765    235   -765 
  -765    135   -765     71 
  -765   -765    235   -765 
  -765   -765    235   -765 
  -765   -765    235   -765 
  -765   -765    235   -765 
--------------------------------------------------------------------------------

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	Motif CGGYGGGG MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.5e+004 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
--------------------------------------------------------------------------------

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	Motif CGGYGGGG MEME-2 regular expression
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CGG[CT]GGGG
--------------------------------------------------------------------------------




Time  0.62 secs.

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MOTIF GCATCRGRBSAGA MEME-3	width =  13  sites =   3  llr = 48  E-value = 1.8e+004
********************************************************************************
--------------------------------------------------------------------------------
	Motif GCATCRGRBSAGA MEME-3 Description
--------------------------------------------------------------------------------
Simplified        A  ::a::3:7::a:a
pos.-specific     C  :a::a:::33:::
probability       G  a::::7a337:a:
matrix            T  :::a::::3::::

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

Multilevel           GCATCGGACGAGA
consensus                 A GGC   
sequence                     T    
                                  
--------------------------------------------------------------------------------

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	Motif GCATCRGRBSAGA MEME-3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                Site   
-------------            ------  ----- ---------            -------------
ce1cg                        +     24  1.86e-08 GGTTTTTGTG GCATCGGGCGAGA ATAGCGCGTG
uxu1                         -     89  2.74e-08       GCTT GCATCGGATGAGA TGGCGTATAA
pbr322                       +     17  1.35e-07 TAACTATGCG GCATCAGAGCAGA TTGTACTGAG
--------------------------------------------------------------------------------

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	Motif GCATCRGRBSAGA MEME-3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
ce1cg                             1.9e-08  23_[+3]_69
uxu1                              2.7e-08  88_[-3]_4
pbr322                            1.3e-07  16_[+3]_76
--------------------------------------------------------------------------------

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	Motif GCATCRGRBSAGA MEME-3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF GCATCRGRBSAGA width=13 seqs=3
ce1cg                    (   24) GCATCGGGCGAGA  1 
uxu1                     (   89) GCATCGGATGAGA  1 
pbr322                   (   17) GCATCAGAGCAGA  1 
//

--------------------------------------------------------------------------------

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	Motif GCATCRGRBSAGA MEME-3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 13 n= 1674 bayes= 8.77981 E= 1.8e+004 
  -823   -823    235   -823 
  -823    235   -823   -823 
   171   -823   -823   -823 
  -823   -823   -823    171 
  -823    235   -823   -823 
    13   -823    176   -823 
  -823   -823    235   -823 
   113   -823     77   -823 
  -823     77     77     13 
  -823     77    176   -823 
   171   -823   -823   -823 
  -823   -823    235   -823 
   171   -823   -823   -823 
--------------------------------------------------------------------------------

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	Motif GCATCRGRBSAGA MEME-3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 13 nsites= 3 E= 1.8e+004 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.333333  0.000000  0.666667  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.666667  0.000000  0.333333  0.000000 
 0.000000  0.333333  0.333333  0.333333 
 0.000000  0.333333  0.666667  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

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	Motif GCATCRGRBSAGA MEME-3 regular expression
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GCATC[GA]G[AG][CGT][GC]AGA
--------------------------------------------------------------------------------




Time  0.86 secs.

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SUMMARY OF MOTIFS
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--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
ce1cg                            3.74e-07  23_[+3(1.86e-08)]_27_[+1(4.87e-06)]_\
    23
ara                              1.77e-04  57_[+1(7.97e-08)]_29
bglr1                            2.94e-02  75_[-1(5.35e-06)]_11
crp                              2.90e-03  65_[+1(1.27e-06)]_21
cya                              9.02e-02  52_[+1(3.16e-05)]_34
deop2                            5.46e-04  59_[-1(3.33e-07)]_27
gale                             3.40e-02  44_[+1(7.68e-06)]_42
ilv                              3.87e-05  4_[+2(2.18e-06)]_29_[+1(8.39e-06)]_\
    45
lac                              9.54e-03  11_[+1(4.43e-06)]_75
male                             2.21e-05  16_[+1(1.97e-06)]_5_[+2(5.56e-06)]_\
    57
malk                             9.33e-03  60_[-1(1.18e-05)]_26
malt                             7.39e-03  40_[-1(1.77e-06)]_46
ompa                             1.58e-02  50_[+1(4.02e-06)]_36
tnaa                             2.01e-03  73_[+1(4.02e-06)]_13
uxu1                             1.81e-06  16_[-1(1.90e-05)]_53_[-3(2.74e-08)]_\
    4
pbr322                           4.03e-07  16_[+3(1.35e-07)]_26_[+1(1.14e-06)]_\
    31
trn9cat                          3.77e-02  83_[-1(1.08e-05)]_3
tdc                              2.06e-02  80_[+1(3.31e-06)]_6
--------------------------------------------------------------------------------

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Stopped because requested number of motifs (3) found.
********************************************************************************

CPU: Timothys-iMac.rd.unr.edu

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