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MEME - Motif discovery tool
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MEME version 4.11.0 (Release date: Thu Nov 26 17:48:49 2015 +1000)

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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DATAFILE= rna_samples.fa
ALPHABET= ACGU
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  
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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 rna_samples.fa -nmotifs 2 -rna -mod oops 

model:  mod=          oops    nmotifs=         2    evt=           inf
object function=  E-value of product of p-values
width:  minw=            8    maxw=           50
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        7    maxsites=        7    wnsites=       0.8
theta:  spmap=         uni    spfuzz=        0.5
global: substring=     yes    branching=      no    wbranch=        no
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=             735    N=               7    shuffle=        -1

sample: seed=            0    ctfrac=         -1    maxwords=       -1
Letter frequencies in dataset:
A 0.313 C 0.174 G 0.190 U 0.322 
Background letter frequencies (from dataset with add-one prior applied):
A 0.313 C 0.175 G 0.191 U 0.322 
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MOTIF  1 MEME	width =  19  sites =   7  llr = 97  E-value = 7.2e-003
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :::364:14:1::91a116
pos.-specific     C  ::1:1:93:4::9:7:4::
probability       G  :3:6:116137:11:::::
matrix            U  a79134::431a::1:494

         bits    2.5                    
                 2.3                    
                 2.0       *     *      
                 1.8       *     *  *   
Relative         1.5 *     *    **  *   
Entropy          1.3 * *   *    *** *   
(19.9 bits)      1.0 ***   **  ****** * 
                 0.8 ****  ** ******* **
                 0.5 ***** ** **********
                 0.3 *******************
                 0.0 -------------------

Multilevel           UUUGAACGACGUCACACUA
consensus             G AUU CUG      U U
sequence                      U         
                                        
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                   Site      
-------------             ----- ---------            -------------------
ara                          58  1.37e-09 ACAUUGAUUA UUUGCACGGCGUCACACUU UGCUAUGCCA
gale                         45  3.90e-08 AUUCCACUAA UUUAUUCCAUGUCACACUU UUCGCAUCUU
deop2                        10  1.66e-07  AGUGAAUUA UUUGAACCAGAUCGCAUUA CAGUGAUGCA
crp                          66  2.14e-07 ACUGCAUGUA UGCAAAGGACGUCACAUUA CCGUGCAGUA
bglr1                        79  6.30e-07 AGUUAAUAAC UGUGAGCAUGGUCAUAUUU UUAUCAAU  
ce1cg                        64  6.75e-07 AGACUGUUUU UUUGAUCGUUUUCACAAAA AUGGAAGUCC
cya                          79  7.76e-07 UUUUAGACCA UUUUUUCGUCGUGAAACUA AAAAAACC  
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
ara                               1.4e-09  57_[1]_29
gale                              3.9e-08  44_[1]_42
deop2                             1.7e-07  9_[1]_77
crp                               2.1e-07  65_[1]_21
bglr1                             6.3e-07  78_[1]_8
ce1cg                             6.8e-07  63_[1]_23
cya                               7.8e-07  78_[1]_8
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=19 seqs=7
ara                      (   58) UUUGCACGGCGUCACACUU  1 
gale                     (   45) UUUAUUCCAUGUCACACUU  1 
deop2                    (   10) UUUGAACCAGAUCGCAUUA  1 
crp                      (   66) UGCAAAGGACGUCACAUUA  1 
bglr1                    (   79) UGUGAGCAUGGUCAUAUUU  1 
ce1cg                    (   64) UUUGAUCGUUUUCACAAAA  1 
cya                      (   79) UUUUUUCGUCGUGAAACUA  1 
//

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

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 19 n= 609 bayes= 6.42626 E= 7.2e-003 
  -945   -945   -945    163 
  -945   -945     58    115 
  -945    -29   -945    141 
   -13   -945    158   -117 
    87    -29   -945    -17 
    45   -945    -42     41 
  -945    229    -42   -945 
  -113     71    158   -945 
    45   -945    -42     41 
  -945    129     58    -17 
  -113   -945    190   -117 
  -945   -945   -945    163 
  -945    229    -42   -945 
   145   -945    -42   -945 
  -113    203   -945   -117 
   168   -945   -945   -945 
  -113    129   -945     41 
  -113   -945   -945    141 
    87   -945   -945     41 
--------------------------------------------------------------------------------

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	Motif 1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 19 nsites= 7 E= 7.2e-003 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.285714  0.714286 
 0.000000  0.142857  0.000000  0.857143 
 0.285714  0.000000  0.571429  0.142857 
 0.571429  0.142857  0.000000  0.285714 
 0.428571  0.000000  0.142857  0.428571 
 0.000000  0.857143  0.142857  0.000000 
 0.142857  0.285714  0.571429  0.000000 
 0.428571  0.000000  0.142857  0.428571 
 0.000000  0.428571  0.285714  0.285714 
 0.142857  0.000000  0.714286  0.142857 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.857143  0.142857  0.000000 
 0.857143  0.000000  0.142857  0.000000 
 0.142857  0.714286  0.000000  0.142857 
 1.000000  0.000000  0.000000  0.000000 
 0.142857  0.428571  0.000000  0.428571 
 0.142857  0.000000  0.000000  0.857143 
 0.571429  0.000000  0.000000  0.428571 
--------------------------------------------------------------------------------

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	Motif 1 regular expression
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U[UG]U[GA][AU][AU]C[GC][AU][CGU]GUCACA[CU]U[AU]
--------------------------------------------------------------------------------




Time  0.13 secs.

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MOTIF  2 MEME	width =   9  sites =   7  llr = 54  E-value = 7.6e+002
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	Motif 2 Description
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Simplified        A  11:6:::1a
pos.-specific     C  :4::::71:
probability       G  9:43:a:1:
matrix            U  :461a:36:

         bits    2.5          
                 2.3      *   
                 2.0      *   
                 1.8 *    *  *
Relative         1.5 *   *** *
Entropy          1.3 *   *** *
(11.1 bits)      1.0 * * *** *
                 0.8 * * *** *
                 0.5 ******* *
                 0.3 *********
                 0.0 ---------

Multilevel           GCUAUGCUA
consensus             UGG  U  
sequence                      
                              
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value              Site 
-------------             ----- ---------            ---------
crp                          13  7.14e-06 CAAAGCGAAA GCUAUGCUA AAACAGUCAG
gale                         75  2.50e-05 UCGCAUCUUU GUUAUGCUA UGGUUAUUUC
ara                          78  3.26e-05 GUCACACUUU GCUAUGCCA UAGCAUUUUU
deop2                        31  1.10e-04 UCGCAUUACA GUGAUGCAA ACUUGUAAGU
cya                           1  1.73e-04          . ACGGUGCUA CACUUGUAUG
ce1cg                        44  3.33e-04 AGAAUAGCGC GUGGUGUGA AAGACUGUUU
bglr1                        27  8.67e-04 UAAUUAUUGG GAUUUGUUA UAUAUAACUU
--------------------------------------------------------------------------------

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	Motif 2 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
crp                               7.1e-06  12_[2]_84
gale                              2.5e-05  74_[2]_22
ara                               3.3e-05  77_[2]_19
deop2                             0.00011  30_[2]_66
cya                               0.00017  [2]_96
ce1cg                             0.00033  43_[2]_53
bglr1                             0.00087  26_[2]_70
--------------------------------------------------------------------------------

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	Motif 2 in BLOCKS format
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BL   MOTIF 2 width=9 seqs=7
crp                      (   13) GCUAUGCUA  1 
gale                     (   75) GUUAUGCUA  1 
ara                      (   78) GCUAUGCCA  1 
deop2                    (   31) GUGAUGCAA  1 
cya                      (    1) ACGGUGCUA  1 
ce1cg                    (   44) GUGGUGUGA  1 
bglr1                    (   27) GAUUUGUUA  1 
//

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

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	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 9 n= 679 bayes= 6.58496 E= 7.6e+002 
  -113   -945    217   -945 
  -113    129   -945     41 
  -945   -945    117     83 
    87   -945     58   -117 
  -945   -945   -945    163 
  -945   -945    239   -945 
  -945    203   -945    -17 
  -113    -29    -42     83 
   168   -945   -945   -945 
--------------------------------------------------------------------------------

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	Motif 2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 9 nsites= 7 E= 7.6e+002 
 0.142857  0.000000  0.857143  0.000000 
 0.142857  0.428571  0.000000  0.428571 
 0.000000  0.000000  0.428571  0.571429 
 0.571429  0.000000  0.285714  0.142857 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.714286  0.000000  0.285714 
 0.142857  0.142857  0.142857  0.571429 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

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	Motif 2 regular expression
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G[CU][UG][AG]UG[CU]UA
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Time  0.17 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                            2.65e-05  63_[1(6.75e-07)]_23
ara                              8.53e-09  57_[1(1.37e-09)]_1_[2(3.26e-05)]_19
bglr1                            5.90e-05  78_[1(6.30e-07)]_8
crp                              2.47e-07  12_[2(7.14e-06)]_44_[1(2.14e-07)]_\
    21
cya                              1.65e-05  78_[1(7.76e-07)]_8
deop2                            2.56e-06  9_[1(1.66e-07)]_77
gale                             1.61e-07  44_[1(3.90e-08)]_11_[2(2.50e-05)]_\
    22
--------------------------------------------------------------------------------

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Stopped because requested number of motifs (2) found.
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CPU: pc

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