********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 5.5.3 (Release date: Sat Jun 10 16:19:38 2023 -0700)

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.

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


********************************************************************************
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.
********************************************************************************


********************************************************************************
TRAINING SET
********************************************************************************
PRIMARY SEQUENCES= common/INO_up800.s
CONTROL SEQUENCES= --none--
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
CHO1                     1.0000    800  CHO2                     1.0000    800  
FAS1                     1.0000    800  FAS2                     1.0000    800  
ACC1                     1.0000    800  INO1                     1.0000    800  
OPI3                     1.0000    800  
********************************************************************************

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

command: meme -p 4 common/INO_up800.s -oc results/meme11 -mod zoops -dna -revcomp -bfile common/yeast.nc.6.freq -nmotifs 2 -objfun classic -minw 8 -nostatus 

model:  mod=         zoops    nmotifs=         2    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=        7    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=            5600    N=               7
sample: seed=            0    hsfrac=          0
        searchsize=   5600    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 common/yeast.nc.6.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
Background model order: 5
********************************************************************************


********************************************************************************
MOTIF GSKGCATGTGAAA MEME-1	width =  13  sites =   7  llr = 101  E-value = 1.9e-001
********************************************************************************
--------------------------------------------------------------------------------
	Motif GSKGCATGTGAAA MEME-1 Description
--------------------------------------------------------------------------------
Simplified        A  1:1::a::1:9a7
pos.-specific     C  :4:3a::::::::
probability       G  9467:::a:a1:3
matrix            T  :13:::a:9::::

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

Multilevel           GCGGCATGTGAAA
consensus             GTC        G
sequence                          
                                  
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif GSKGCATGTGAAA MEME-1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                Site   
-------------            ------  ----- ---------            -------------
INO1                         +    620  1.21e-08 GCGGCTAAAT GCGGCATGTGAAA AGTATTGTCT
FAS1                         -     94  1.87e-08 GCTTGGCTGG GCGGCATGTGAAG TTTTTGGCCG
ACC1                         -     82  6.62e-08 GCGCGCGGCC GGGCCATGTGAAG ATTTTAACGG
CHO2                         -    353  1.05e-07 AATAATGAAT GCGGCATGAGAAA AGTGTGGCAA
CHO1                         -    639  1.69e-07 TCTTTAGATG GGTCCATGTGAAA GCTCAAAGGC
FAS2                         -    566  5.62e-07 GGCGAATGAG GTAGCATGTGAAA ACGCGGGAGA
OPI3                         +    585  1.08e-06 TGTCAATGAG AGTGCATGTGGAA AGTTGCACCG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif GSKGCATGTGAAA MEME-1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
INO1                              1.2e-08  619_[+1]_168
FAS1                              1.9e-08  93_[-1]_694
ACC1                              6.6e-08  81_[-1]_706
CHO2                              1.1e-07  352_[-1]_435
CHO1                              1.7e-07  638_[-1]_149
FAS2                              5.6e-07  565_[-1]_222
OPI3                              1.1e-06  584_[+1]_203
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif GSKGCATGTGAAA MEME-1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF GSKGCATGTGAAA width=13 seqs=7
INO1                     (  620) GCGGCATGTGAAA  1 
FAS1                     (   94) GCGGCATGTGAAG  1 
ACC1                     (   82) GGGCCATGTGAAG  1 
CHO2                     (  353) GCGGCATGAGAAA  1 
CHO1                     (  639) GGTCCATGTGAAA  1 
FAS2                     (  566) GTAGCATGTGAAA  1 
OPI3                     (  585) AGTGCATGTGGAA  1 
//

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

--------------------------------------------------------------------------------
	Motif GSKGCATGTGAAA MEME-1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 13 n= 5516 bayes= 9.62022 E= 1.9e-001 
  -118   -945    229   -945 
  -945    129    129   -118 
  -118   -945    170    -18 
  -945     70    202   -945 
  -945    251   -945   -945 
   162   -945   -945   -945 
  -945   -945   -945    162 
  -945   -945    251   -945 
  -118   -945   -945    140 
  -945   -945    251   -945 
   140   -945    -30   -945 
   162   -945   -945   -945 
   114   -945     70   -945 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif GSKGCATGTGAAA MEME-1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 13 nsites= 7 E= 1.9e-001 
 0.142857  0.000000  0.857143  0.000000 
 0.000000  0.428571  0.428571  0.142857 
 0.142857  0.000000  0.571429  0.285714 
 0.000000  0.285714  0.714286  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  0.000000  1.000000  0.000000 
 0.142857  0.000000  0.000000  0.857143 
 0.000000  0.000000  1.000000  0.000000 
 0.857143  0.000000  0.142857  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.714286  0.000000  0.285714  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif GSKGCATGTGAAA MEME-1 regular expression
--------------------------------------------------------------------------------
G[CG][GT][GC]CATGTGAA[AG]
--------------------------------------------------------------------------------




Time  0.79 secs.

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


********************************************************************************
MOTIF TTGACWCYTGCYCWG MEME-2	width =  15  sites =   7  llr = 99  E-value = 5.4e+001
********************************************************************************
--------------------------------------------------------------------------------
	Motif TTGACWCYTGCYCWG MEME-2 Description
--------------------------------------------------------------------------------
Simplified        A  :::9:63::11:13:
pos.-specific     C  ::3:a:76:19471:
probability       G  ::7::1::17::11a
matrix            T  aa:1:3:49::6:4:

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

Multilevel           TTGACACCTGCTCTG
consensus              C  TAT   C A 
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TTGACWCYTGCYCWG MEME-2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
CHO2                         +    104  7.20e-10 AGTTCTTACT TTGACACCTGCCCAG ATCCAAAGTT
OPI3                         -    566  2.56e-08 TGCACTCTCA TTGACACCTACCCTG GTCATCAAGG
ACC1                         -    585  1.59e-07 GGGAAGTTTC TTGTCTCTTGCTCTG AATCTGAATT
CHO1                         +     30  2.05e-07 ACAATATTAT TTGACACTTGATCAG CAGCAAAATA
FAS1                         +     54  3.85e-07 GCAGGCACGG TTCACTACTCCCCTG GCCTCCAACA
FAS2                         -    272  5.11e-07 TTAACGCGTT TTGACAACGGCTGGG ACAACAACGA
INO1                         +    214  8.01e-07 CCAGCAATCA TTCACGCTTGCTACG TTGTATATGA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TTGACWCYTGCYCWG MEME-2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
CHO2                              7.2e-10  103_[+2]_682
OPI3                              2.6e-08  565_[-2]_220
ACC1                              1.6e-07  584_[-2]_201
CHO1                                2e-07  29_[+2]_756
FAS1                              3.8e-07  53_[+2]_732
FAS2                              5.1e-07  271_[-2]_514
INO1                                8e-07  213_[+2]_572
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TTGACWCYTGCYCWG MEME-2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF TTGACWCYTGCYCWG width=15 seqs=7
CHO2                     (  104) TTGACACCTGCCCAG  1 
OPI3                     (  566) TTGACACCTACCCTG  1 
ACC1                     (  585) TTGTCTCTTGCTCTG  1 
CHO1                     (   30) TTGACACTTGATCAG  1 
FAS1                     (   54) TTCACTACTCCCCTG  1 
FAS2                     (  272) TTGACAACGGCTGGG  1 
INO1                     (  214) TTCACGCTTGCTACG  1 
//

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

--------------------------------------------------------------------------------
	Motif TTGACWCYTGCYCWG MEME-2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 5502 bayes= 9.61655 E= 5.4e+001 
  -945   -945   -945    162 
  -945   -945   -945    162 
  -945     70    202   -945 
   140   -945   -945   -118 
  -945    251   -945   -945 
    82   -945    -30    -18 
   -18    202   -945   -945 
  -945    170   -945     40 
  -945   -945    -30    140 
  -118    -30    202   -945 
  -118    229   -945   -945 
  -945    129   -945     82 
  -118    202    -30   -945 
   -18    -30    -30     40 
  -945   -945    251   -945 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TTGACWCYTGCYCWG MEME-2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 7 E= 5.4e+001 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.285714  0.714286  0.000000 
 0.857143  0.000000  0.000000  0.142857 
 0.000000  1.000000  0.000000  0.000000 
 0.571429  0.000000  0.142857  0.285714 
 0.285714  0.714286  0.000000  0.000000 
 0.000000  0.571429  0.000000  0.428571 
 0.000000  0.000000  0.142857  0.857143 
 0.142857  0.142857  0.714286  0.000000 
 0.142857  0.857143  0.000000  0.000000 
 0.000000  0.428571  0.000000  0.571429 
 0.142857  0.714286  0.142857  0.000000 
 0.285714  0.142857  0.142857  0.428571 
 0.000000  0.000000  1.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TTGACWCYTGCYCWG MEME-2 regular expression
--------------------------------------------------------------------------------
TT[GC]AC[AT][CA][CT]TGC[TC]C[TA]G
--------------------------------------------------------------------------------




Time  1.44 secs.

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


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

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
CHO1                             1.48e-06  29_[+2(2.05e-07)]_594_\
    [-1(1.69e-07)]_149
CHO2                             4.39e-09  103_[+2(7.20e-10)]_234_\
    [-1(1.05e-07)]_435
FAS1                             3.35e-07  53_[+2(3.85e-07)]_25_[-1(1.87e-08)]_\
    694
FAS2                             1.08e-05  271_[-2(5.11e-07)]_279_\
    [-1(5.62e-07)]_222
ACC1                             4.83e-07  81_[-1(6.62e-08)]_490_\
    [-2(1.59e-07)]_201
INO1                             4.45e-07  213_[+2(8.01e-07)]_342_\
    [+1(1.52e-05)]_36_[+1(1.21e-08)]_53_[-1(5.60e-06)]_102
OPI3                             1.20e-06  314_[-1(3.24e-05)]_238_\
    [-2(2.56e-08)]_4_[+1(1.08e-06)]_203
--------------------------------------------------------------------------------

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


********************************************************************************
Stopped because requested number of motifs (2) found.
********************************************************************************

CPU: Timothys-iMac.local

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