********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 5.0.5 (Release date: Mon Mar 18 20:12:19 2019 -0700)

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

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********************************************************************************
REFERENCE
********************************************************************************
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
********************************************************************************
PRIMARY SEQUENCES= tmp/ArgR.fasta
CONTROL SEQUENCES= --none--
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
argA                     1.0000    600  argCBH                   1.0000    600  
argD                     1.0000    600  argE                     1.0000    600  
argF                     1.0000    600  argG                     1.0000    600  
argI                     1.0000    600  artJ                     1.0000    600  
carAB                    1.0000    600  dtpD                     1.0000    600  
xynR                     1.0000    600  
********************************************************************************

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COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme tmp/ArgR.fasta -oc tmp/ArgR -dna -mod zoops -nmotifs 5 -evt 0.001 -minw 6 -maxw 40 -allw -minsites 3 -mpi 

model:  mod=         zoops    nmotifs=         5    evt=         0.001
objective function:           em=       E-value of product of p-values
                              starts=   E-value of product of p-values
strands: +
width:  minw=            6    maxw=           40
nsites: minsites=        3    maxsites=       11    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=            6600    N=              11
sample: seed=            0    hsfrac=          0
        searchsize=   6600    norand=         no    csites=       1000
Letter frequencies in dataset:
A 0.266 C 0.233 G 0.236 T 0.265 
Background letter frequencies (from file dataset with add-one prior applied):
A 0.266 C 0.233 G 0.236 T 0.265 
Background model order: 0
********************************************************************************


********************************************************************************
MOTIF TGAATWWAHATKCAVTWWWTWTGMATAAAWATWCAHTRR MEME-1	width =  39  sites =  10  llr = 284  E-value = 1.7e-030
********************************************************************************
--------------------------------------------------------------------------------
	Motif TGAATWWAHATKCAVTWWWTWTGMATAAAWATWCAHTRR MEME-1 Description
--------------------------------------------------------------------------------
Simplified        A  11a913684a11:93255526::57:8a74a23:82255
pos.-specific     C  :2:::1::2:11a:3:1::1:1:3:::::1:::9:4:::
probability       G  :6::11:::::5::3:::1:1:a12:2:::::1::1:34
matrix            T  91:185424:83:118454739:11a::35:86123821

         bits    2.1             *         *                
                 1.9   *      *  *         *  * *  *        
                 1.7   *      *  *         *  * *  *  *     
                 1.5 * **     *  **       **  * *  *  *     
Relative         1.3 * **   * *  ** *     **  ***  ** ** *  
Entropy          1.0 * ***  * ** ** *     **  **** ** ** *  
(41.0 bits)      0.8 * *** ** ** ** * * * ** ***** ** ** *  
                 0.6 * *** ** ** ** ******** *********** * *
                 0.4 ***** ******** ******** *********** ***
                 0.2 ***************************************
                 0.0 ---------------------------------------

Multilevel           TGAATTAAAATGCAATAAATATGAATAAATATTCACTAA
consensus             C   ATTT  T  CATTTAT  CG G TA AA TTAGG
sequence                     C     G                    A T 
                                                            
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TGAATWWAHATKCAVTWWWTWTGMATAAAWATWCAHTRR MEME-1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                             Site                
-------------             ----- ---------            ---------------------------------------
argE                        129  1.89e-16 CATGATAGTA TCAATATTCATGCAGTATTTATGAATAAAAATACACTAA CGTTGAGCGT
argCBH                      376  1.89e-16 CATGATAGTA TCAATATTCATGCAGTATTTATGAATAAAAATACACTAA CGTTGAGCGT
argF                        130  6.79e-16 CGCCACTTAT TGAATTAAAATTCACTTTATATGTGTAATTATTCATTTG CAACCCCATT
argI                        128  9.75e-16 AACGCCTCAA TGAATTAAAATTCAATTTATATGGATGATTATTCATTTG CAAGTCTAAA
carAB                       454  3.02e-14 GTCATCATTG TGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGG AGGGTGTTTT
argD                        133  6.68e-14 TAAACAAATG TGAAATTATAACCACAAAATATGCATAAAAAATCACTAA ATGGCAATCA
argG                        413  2.07e-13 AAAAGATGAT TAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGA GAGCGGAAAT
artJ                        172  1.63e-12 TGCCATCAAG TGAATTTATATGCAATAAACATGATTAAATAATTTAAAT GAAATAAAAA
argA                        454  2.78e-12 GCGAAAAAAC AGAATAAAAATACACTAATTTCGAATAATCATGCAAAGA GGTGTGCCGT
dtpD                        193  1.11e-11 ATCTGATTAT TTATGCAATATGCTGTCTGATTGCATAAATATACATTAG CTGAAGCGTG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TGAATWWAHATKCAVTWWWTWTGMATAAAWATWCAHTRR MEME-1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
argE                              1.9e-16  128_[+1]_433
argCBH                            1.9e-16  375_[+1]_186
argF                              6.8e-16  129_[+1]_432
argI                              9.7e-16  127_[+1]_434
carAB                               3e-14  453_[+1]_108
argD                              6.7e-14  132_[+1]_429
argG                              2.1e-13  412_[+1]_149
artJ                              1.6e-12  171_[+1]_390
argA                              2.8e-12  453_[+1]_108
dtpD                              1.1e-11  192_[+1]_369
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TGAATWWAHATKCAVTWWWTWTGMATAAAWATWCAHTRR MEME-1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF TGAATWWAHATKCAVTWWWTWTGMATAAAWATWCAHTRR width=39 seqs=10
argE                     (  129) TCAATATTCATGCAGTATTTATGAATAAAAATACACTAA  1 
argCBH                   (  376) TCAATATTCATGCAGTATTTATGAATAAAAATACACTAA  1 
argF                     (  130) TGAATTAAAATTCACTTTATATGTGTAATTATTCATTTG  1 
argI                     (  128) TGAATTAAAATTCAATTTATATGGATGATTATTCATTTG  1 
carAB                    (  454) TGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGG  1 
argD                     (  133) TGAAATTATAACCACAAAATATGCATAAAAAATCACTAA  1 
argG                     (  413) TAAATGAAAACTCATTTATTTTGCATAAAAATTCAGTGA  1 
artJ                     (  172) TGAATTTATATGCAATAAACATGATTAAATAATTTAAAT  1 
argA                     (  454) AGAATAAAAATACACTAATTTCGAATAATCATGCAAAGA  1 
dtpD                     (  193) TTATGCAATATGCTGTCTGATTGCATAAATATACATTAG  1 
//

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

--------------------------------------------------------------------------------
	Motif TGAATWWAHATKCAVTWWWTWTGMATAAAWATWCAHTRR MEME-1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 39 n= 6182 bayes= 9.82674 E= 1.7e-030 
  -141   -997   -997    177 
  -141    -22    134   -140 
   191   -997   -997   -997 
   176   -997   -997   -140 
  -141   -997   -124    160 
    17   -122   -124     92 
   117   -997   -997     60 
   159   -997   -997    -40 
    59    -22   -997     60 
   191   -997   -997   -997 
  -141   -122   -997    160 
  -141   -122    108     18 
  -997    210   -997   -997 
   176   -997   -997   -140 
    17     36     35   -140 
   -41   -997   -997    160 
    91   -122   -997     60 
    91   -997   -997     92 
    91   -997   -124     60 
   -41   -122   -997    140 
   117   -997   -124     18 
  -997   -122   -997    177 
  -997   -997    208   -997 
    91     36   -124   -140 
   139   -997    -24   -140 
  -997   -997   -997    192 
   159   -997    -24   -997 
   191   -997   -997   -997 
   139   -997   -997     18 
    59   -122   -997     92 
   191   -997   -997   -997 
   -41   -997   -997    160 
    17   -997   -124    118 
  -997    195   -997   -140 
   159   -997   -997    -40 
   -41     78   -124     18 
   -41   -997   -997    160 
    91   -997     35    -40 
    91   -997     76   -140 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TGAATWWAHATKCAVTWWWTWTGMATAAAWATWCAHTRR MEME-1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 39 nsites= 10 E= 1.7e-030 
 0.100000  0.000000  0.000000  0.900000 
 0.100000  0.200000  0.600000  0.100000 
 1.000000  0.000000  0.000000  0.000000 
 0.900000  0.000000  0.000000  0.100000 
 0.100000  0.000000  0.100000  0.800000 
 0.300000  0.100000  0.100000  0.500000 
 0.600000  0.000000  0.000000  0.400000 
 0.800000  0.000000  0.000000  0.200000 
 0.400000  0.200000  0.000000  0.400000 
 1.000000  0.000000  0.000000  0.000000 
 0.100000  0.100000  0.000000  0.800000 
 0.100000  0.100000  0.500000  0.300000 
 0.000000  1.000000  0.000000  0.000000 
 0.900000  0.000000  0.000000  0.100000 
 0.300000  0.300000  0.300000  0.100000 
 0.200000  0.000000  0.000000  0.800000 
 0.500000  0.100000  0.000000  0.400000 
 0.500000  0.000000  0.000000  0.500000 
 0.500000  0.000000  0.100000  0.400000 
 0.200000  0.100000  0.000000  0.700000 
 0.600000  0.000000  0.100000  0.300000 
 0.000000  0.100000  0.000000  0.900000 
 0.000000  0.000000  1.000000  0.000000 
 0.500000  0.300000  0.100000  0.100000 
 0.700000  0.000000  0.200000  0.100000 
 0.000000  0.000000  0.000000  1.000000 
 0.800000  0.000000  0.200000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.700000  0.000000  0.000000  0.300000 
 0.400000  0.100000  0.000000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 0.200000  0.000000  0.000000  0.800000 
 0.300000  0.000000  0.100000  0.600000 
 0.000000  0.900000  0.000000  0.100000 
 0.800000  0.000000  0.000000  0.200000 
 0.200000  0.400000  0.100000  0.300000 
 0.200000  0.000000  0.000000  0.800000 
 0.500000  0.000000  0.300000  0.200000 
 0.500000  0.000000  0.400000  0.100000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TGAATWWAHATKCAVTWWWTWTGMATAAAWATWCAHTRR MEME-1 regular expression
--------------------------------------------------------------------------------
T[GC]AAT[TA][AT][AT][ATC]AT[GT]CA[ACG][TA][AT][AT][AT][TA][AT]TG[AC][AG]T[AG]A[AT][TA]A[TA][TA]C[AT][CTA][TA][AGT][AG]
--------------------------------------------------------------------------------




Time  1.42 secs.

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********************************************************************************
MOTIF GMAYASGCWSVTYGYGGVTGHCHGMDGCNACGCTGGCGY MEME-2	width =  39  sites =   5  llr = 162  E-value = 1.5e-004
********************************************************************************
--------------------------------------------------------------------------------
	Motif GMAYASGCWSVTYGYGGVTGHCHGMDGCNACGCTGGCGY MEME-2 Description
--------------------------------------------------------------------------------
Simplified        A  :6a:8::24:42:::::2::4:4:442:28:2:::2:::
pos.-specific     C  :4:62628:44:4242:42:4a226::a228:a::2a26
probability       G  a::::48::622:8:6a4:a:::8:48:2:26:286:8:
matrix            T  :::4::::6::66:62::8:2:4::2::4::2:82:::4

         bits    2.1 *               *  * *     *    *   *  
                 1.9 * *             *  * *     *    *   *  
                 1.7 * *             *  * *     *    *   *  
                 1.5 * *             *  * *     *  * *   *  
Relative         1.3 * * * **     *  * ** * *  ** ** *** ** 
Entropy          1.0 ******** *  *** * ** * ** ** ** *** ***
(46.7 bits)      0.8 **********  *** * ** * ** ** ** *** ***
                 0.6 ********** ********* * ** ** **********
                 0.4 **************************** **********
                 0.2 **************************** **********
                 0.0 ---------------------------------------

Multilevel           GAACACGCTGATTGTGGCTGACAGCAGCTACGCTGGCGC
consensus             C TCGCAACCACCCC GC C TCAGA ACGA GTA CT
sequence                       GG   T A  T C  T  C  T   C   
                                                 G          
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif GMAYASGCWSVTYGYGGVTGHCHGMDGCNACGCTGGCGY MEME-2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name             Start   P-value                             Site                
-------------             ----- ---------            ---------------------------------------
argE                        259  4.24e-22 CCCCGATGTT GAATACGCTGATTGTGGGTGCCAGCGGCTACGCTGGCGC AGAGCTAGTG
argCBH                      506  4.24e-22 CCCCGATGTT GAATACGCTGATTGTGGGTGCCAGCGGCTACGCTGGCGC AGAGCTAGTG
artJ                        306  1.00e-15 GCCGCATCCG GCACAGGCACCGTGCTGATGTCTGATGCGACGCTGGCGC GTCTTATCAG
argA                        152  1.64e-13 GGCCAGACGC GCACCGCCACGACCTGGCTGACCGCAGCCAGACTGACCT GACTTACGCT
xynR                        302  2.76e-13 CCGCCTGGTC GAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGT CACCTCCATC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif GMAYASGCWSVTYGYGGVTGHCHGMDGCNACGCTGGCGY MEME-2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
argE                              4.2e-22  258_[+2]_303
argCBH                            4.2e-22  505_[+2]_56
artJ                                1e-15  305_[+2]_256
argA                              1.6e-13  151_[+2]_410
xynR                              2.8e-13  301_[+2]_260
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif GMAYASGCWSVTYGYGGVTGHCHGMDGCNACGCTGGCGY MEME-2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF GMAYASGCWSVTYGYGGVTGHCHGMDGCNACGCTGGCGY width=39 seqs=5
argE                     (  259) GAATACGCTGATTGTGGGTGCCAGCGGCTACGCTGGCGC  1 
argCBH                   (  506) GAATACGCTGATTGTGGGTGCCAGCGGCTACGCTGGCGC  1 
artJ                     (  306) GCACAGGCACCGTGCTGATGTCTGATGCGACGCTGGCGC  1 
argA                     (  152) GCACCGCCACGACCTGGCTGACCGCAGCCAGACTGACCT  1 
xynR                     (  302) GAACACGATGCTCGCCGCCGACTCAAACACCTCGTCCGT  1 
//

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

--------------------------------------------------------------------------------
	Motif GMAYASGCWSVTYGYGGVTGHCHGMDGCNACGCTGGCGY MEME-2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 39 n= 6182 bayes= 10.8275 E= 1.5e-004 
  -897   -897    208   -897 
   117     78   -897   -897 
   191   -897   -897   -897 
  -897    136   -897     60 
   159    -22   -897   -897 
  -897    136     76   -897 
  -897    -22    176   -897 
   -41    178   -897   -897 
    59   -897   -897    118 
  -897     78    134   -897 
    59     78    -24   -897 
   -41   -897    -24    118 
  -897     78   -897    118 
  -897    -22    176   -897 
  -897     78   -897    118 
  -897    -22    134    -40 
  -897   -897    208   -897 
   -41     78     76   -897 
  -897    -22   -897    159 
  -897   -897    208   -897 
    59     78   -897    -40 
  -897    210   -897   -897 
    59    -22   -897     60 
  -897    -22    176   -897 
    59    136   -897   -897 
    59   -897     76    -40 
   -41   -897    176   -897 
  -897    210   -897   -897 
   -41    -22    -24     60 
   159    -22   -897   -897 
  -897    178    -24   -897 
   -41   -897    134    -40 
  -897    210   -897   -897 
  -897   -897    -24    159 
  -897   -897    176    -40 
   -41    -22    134   -897 
  -897    210   -897   -897 
  -897    -22    176   -897 
  -897    136   -897     60 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif GMAYASGCWSVTYGYGGVTGHCHGMDGCNACGCTGGCGY MEME-2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 39 nsites= 5 E= 1.5e-004 
 0.000000  0.000000  1.000000  0.000000 
 0.600000  0.400000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.600000  0.000000  0.400000 
 0.800000  0.200000  0.000000  0.000000 
 0.000000  0.600000  0.400000  0.000000 
 0.000000  0.200000  0.800000  0.000000 
 0.200000  0.800000  0.000000  0.000000 
 0.400000  0.000000  0.000000  0.600000 
 0.000000  0.400000  0.600000  0.000000 
 0.400000  0.400000  0.200000  0.000000 
 0.200000  0.000000  0.200000  0.600000 
 0.000000  0.400000  0.000000  0.600000 
 0.000000  0.200000  0.800000  0.000000 
 0.000000  0.400000  0.000000  0.600000 
 0.000000  0.200000  0.600000  0.200000 
 0.000000  0.000000  1.000000  0.000000 
 0.200000  0.400000  0.400000  0.000000 
 0.000000  0.200000  0.000000  0.800000 
 0.000000  0.000000  1.000000  0.000000 
 0.400000  0.400000  0.000000  0.200000 
 0.000000  1.000000  0.000000  0.000000 
 0.400000  0.200000  0.000000  0.400000 
 0.000000  0.200000  0.800000  0.000000 
 0.400000  0.600000  0.000000  0.000000 
 0.400000  0.000000  0.400000  0.200000 
 0.200000  0.000000  0.800000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.200000  0.200000  0.200000  0.400000 
 0.800000  0.200000  0.000000  0.000000 
 0.000000  0.800000  0.200000  0.000000 
 0.200000  0.000000  0.600000  0.200000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.200000  0.800000 
 0.000000  0.000000  0.800000  0.200000 
 0.200000  0.200000  0.600000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.200000  0.800000  0.000000 
 0.000000  0.600000  0.000000  0.400000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif GMAYASGCWSVTYGYGGVTGHCHGMDGCNACGCTGGCGY MEME-2 regular expression
--------------------------------------------------------------------------------
G[AC]A[CT][AC][CG][GC][CA][TA][GC][ACG][TAG][TC][GC][TC][GCT]G[CGA][TC]G[ACT]C[ATC][GC][CA][AGT][GA]C[TACG][AC][CG][GAT]C[TG][GT][GAC]C[GC][CT]
--------------------------------------------------------------------------------




Time  2.90 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
argA                             6.42e-18  151_[+2(1.64e-13)]_263_\
    [+1(2.78e-12)]_108
argCBH                           1.87e-30  161_[+2(9.14e-05)]_175_\
    [+1(1.89e-16)]_91_[+2(4.24e-22)]_56
argD                             5.70e-10  132_[+1(6.68e-14)]_429
argE                             1.87e-30  128_[+1(1.89e-16)]_91_\
    [+2(4.24e-22)]_303
argF                             9.15e-12  129_[+1(6.79e-16)]_432
argG                             1.07e-09  272_[+1(8.17e-05)]_101_\
    [+1(2.07e-13)]_149
argI                             1.23e-11  127_[+1(9.75e-16)]_127_\
    [+1(9.99e-05)]_268
artJ                             2.58e-20  171_[+1(1.63e-12)]_95_\
    [+2(1.00e-15)]_256
carAB                            3.38e-10  34_[+1(2.63e-05)]_63_[+1(7.06e-05)]_\
    278_[+1(3.02e-14)]_108
dtpD                             8.19e-08  192_[+1(1.11e-11)]_369
xynR                             1.95e-09  301_[+2(2.76e-13)]_260
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because motif E-value > 1.00e-03.
********************************************************************************

CPU: sbrg-sastry

********************************************************************************
