********************************************************************************
MEME - Motif discovery tool
********************************************************************************
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.

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


********************************************************************************
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/meme12 -mod anr -dna -revcomp -bfile common/yeast.nc.6.freq -nmotifs 2 -objfun classic -minw 8 -nostatus 

model:  mod=           anr    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=       35    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 TTCACATGSMVCM MEME-1	width =  13  sites =  10  llr = 135  E-value = 9.1e-004
********************************************************************************
--------------------------------------------------------------------------------
	Motif TTCACATGSMVCM MEME-1 Description
--------------------------------------------------------------------------------
Simplified        A  :::9:a:::43:4
pos.-specific     C  :1a:a:1:65395
probability       G  :::::::94:4:1
matrix            T  a9:1::91:1:1:

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

Multilevel           TTCACATGCCGCC
consensus                    GAA A
sequence                       C  
                                  
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TTCACATGSMVCM MEME-1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                Site   
-------------            ------  ----- ---------            -------------
FAS1                         +     95  3.29e-09 GGCCAAAAAC TTCACATGCCGCC CAGCCAAGCA
INO1                         -    619  3.13e-08 GACAATACTT TTCACATGCCGCA TTTAGCCGCC
CHO1                         +    640  7.37e-08 CCTTTGAGCT TTCACATGGACCC ATCTAAAGAT
INO1                         +    687  1.72e-07 ACTTATTTAA TTCACATGGAGCA GAGAAAGCGC
ACC1                         +     83  1.88e-07 CGTTAAAATC TTCACATGGCCCG GCCGCGCGCG
CHO1                         +    611  3.43e-07 ACTTTGAACG TTCACACGGCACC CTCACGCCTT
FAS2                         +    567  4.16e-07 CTCCCGCGTT TTCACATGCTACC TCATTCGCCT
CHO2                         +    354  4.16e-07 TGCCACACTT TTCTCATGCCGCA TTCATTATTC
INO1                         -    570  2.24e-06 CTCCGCATAT TTCACATTCAACA CTTTCGATTC
OPI3                         -    584  2.44e-06 GGTGCAACTT TCCACATGCACTC TCATTGACAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TTCACATGSMVCM MEME-1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
FAS1                              3.3e-09  94_[+1]_693
INO1                              1.7e-07  569_[-1]_36_[-1]_55_[+1]_101
CHO1                              3.4e-07  610_[+1]_16_[+1]_148
ACC1                              1.9e-07  82_[+1]_705
FAS2                              4.2e-07  566_[+1]_221
CHO2                              4.2e-07  353_[+1]_434
OPI3                              2.4e-06  583_[-1]_204
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TTCACATGSMVCM MEME-1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF TTCACATGSMVCM width=13 seqs=10
FAS1                     (   95) TTCACATGCCGCC  1 
INO1                     (  619) TTCACATGCCGCA  1 
CHO1                     (  640) TTCACATGGACCC  1 
INO1                     (  687) TTCACATGGAGCA  1 
ACC1                     (   83) TTCACATGGCCCG  1 
CHO1                     (  611) TTCACACGGCACC  1 
FAS2                     (  567) TTCACATGCTACC  1 
CHO2                     (  354) TTCTCATGCCGCA  1 
INO1                     (  570) TTCACATTCAACA  1 
OPI3                     (  584) TCCACATGCACTC  1 
//

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

--------------------------------------------------------------------------------
	Motif TTCACATGSMVCM MEME-1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 13 n= 5516 bayes= 9.35682 E= 9.1e-004 
  -997   -997   -997    162 
  -997    -81   -997    147 
  -997    251   -997   -997 
   147   -997   -997   -169 
  -997    251   -997   -997 
   162   -997   -997   -997 
  -997    -81   -997    147 
  -997   -997    236   -169 
  -997    177    119   -997 
    30    151   -997   -169 
   -11     77    119   -997 
  -997    236   -997   -169 
    30    151    -81   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TTCACATGSMVCM MEME-1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 13 nsites= 10 E= 9.1e-004 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.100000  0.000000  0.900000 
 0.000000  1.000000  0.000000  0.000000 
 0.900000  0.000000  0.000000  0.100000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.100000  0.000000  0.900000 
 0.000000  0.000000  0.900000  0.100000 
 0.000000  0.600000  0.400000  0.000000 
 0.400000  0.500000  0.000000  0.100000 
 0.300000  0.300000  0.400000  0.000000 
 0.000000  0.900000  0.000000  0.100000 
 0.400000  0.500000  0.100000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif TTCACATGSMVCM MEME-1 regular expression
--------------------------------------------------------------------------------
TTCACATG[CG][CA][GAC]C[CA]
--------------------------------------------------------------------------------




Time  1.38 secs.

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


********************************************************************************
MOTIF VDMBNCCMSHTSWVYACYGKC MEME-2	width =  21  sites =  12  llr = 172  E-value = 2.0e+000
********************************************************************************
--------------------------------------------------------------------------------
	Motif VDMBNCCMSHTSWVYACYGKC MEME-2 Description
--------------------------------------------------------------------------------
Simplified        A  345:32:5:3::33:7:::::
pos.-specific     C  4:3336936435:45:86::8
probability       G  3324331:4:152321::a63
matrix            T  :3:32::2:37:5:3324:4:

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

Multilevel           CAAGACCACCTCTCCACCGGC
consensus            ATCCCG CGACGAATT T TG
sequence             GG TG    T   G       
                                          
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif VDMBNCCMSHTSWVYACYGKC MEME-2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site       
-------------            ------  ----- ---------            ---------------------
INO1                         -    369  1.17e-09 TGTTGTCCAT CAAGGGCACATCGGCACCGGC CTCATCGTCT
FAS2                         +    710  4.56e-09 GAAGGTTACA CAAGACCACATCACCACTGTC GTGCTTTTCT
INO1                         +    283  6.95e-08 AGACATGCGA CTGCGCCCGCCGTAGACCGTG ACCTGGAAGC
INO1                         -    536  7.72e-08 TCGATTCCGC ATCCAACCCCGGAACACCGGC ACGTATTTCA
INO1                         +    399  8.57e-08 GATGGACAAC AAACAACAGCTCTCTTCCGGC CGTACTTAGT
INO1                         -    122  1.40e-07 CATACCCTTA CGCTTCCAGACGGCCACTGGG GGAATGAAAA
OPI3                         -    504  2.39e-07 CGAATTATAC GGCGGCGCCATCACTACTGTC GTCCCACCTG
OPI3                         +    289  2.60e-07 TTCCCATTTG GTGGTCCCGTTCAACTCCGTC AGGTCTTCCA
ACC1                         +    217  2.60e-07 AGAAGAACAG CACTCCCAGTCGTATTCTGGC ACAGTATAGC
INO1                         +    703  3.58e-07 TGGAGCAGAG AAAGCGCACCTCTGCGTTGGC GGCAATGTTA
OPI3                         +    343  4.17e-07 AGCCTCCTTC AGATCGCTCTTGTCGACCGTC TCCAAGAGAT
OPI3                         +    441  4.49e-07 GGGAATTGAC GTACACCTCCTGTGTATCGGG GACTTCTCTT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif VDMBNCCMSHTSWVYACYGKC MEME-2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
INO1                              8.6e-08  121_[-2]_140_[+2]_65_[-2]_9_[+2]_
                                           116_[-2]_146_[+2]_77
FAS2                              4.6e-09  709_[+2]_70
OPI3                              2.4e-07  288_[+2]_33_[+2]_77_[+2]_42_[-2]_276
ACC1                              2.6e-07  216_[+2]_563
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif VDMBNCCMSHTSWVYACYGKC MEME-2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF VDMBNCCMSHTSWVYACYGKC width=21 seqs=12
INO1                     (  369) CAAGGGCACATCGGCACCGGC  1 
FAS2                     (  710) CAAGACCACATCACCACTGTC  1 
INO1                     (  283) CTGCGCCCGCCGTAGACCGTG  1 
INO1                     (  536) ATCCAACCCCGGAACACCGGC  1 
INO1                     (  399) AAACAACAGCTCTCTTCCGGC  1 
INO1                     (  122) CGCTTCCAGACGGCCACTGGG  1 
OPI3                     (  504) GGCGGCGCCATCACTACTGTC  1 
OPI3                     (  289) GTGGTCCCGTTCAACTCCGTC  1 
ACC1                     (  217) CACTCCCAGTCGTATTCTGGC  1 
INO1                     (  703) AAAGCGCACCTCTGCGTTGGC  1 
OPI3                     (  343) AGATCGCTCTTGTCGACCGTC  1 
OPI3                     (  441) GTACACCTCCTGTGTATCGGG  1 
//

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

--------------------------------------------------------------------------------
	Motif VDMBNCCMSHTSWVYACYGKC MEME-2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 21 n= 5460 bayes= 9.92778 E= 2.0e+000 
     4    125     51  -1023 
    36  -1023     51      4 
    62     92     -8  -1023 
 -1023     92    125    -38 
     4     51     51    -96 
   -96    173     51  -1023 
 -1023    238   -107  -1023 
    62     92  -1023    -96 
 -1023    173    125  -1023 
     4    125  -1023    -38 
 -1023     51   -107    104 
 -1023    151    151  -1023 
     4  -1023     -8     62 
     4    125     51  -1023 
 -1023    151     -8      4 
   104  -1023   -107    -38 
 -1023    225  -1023    -96 
 -1023    173  -1023     36 
 -1023  -1023    251  -1023 
 -1023  -1023    173     36 
 -1023    209     51  -1023 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif VDMBNCCMSHTSWVYACYGKC MEME-2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 21 nsites= 12 E= 2.0e+000 
 0.333333  0.416667  0.250000  0.000000 
 0.416667  0.000000  0.250000  0.333333 
 0.500000  0.333333  0.166667  0.000000 
 0.000000  0.333333  0.416667  0.250000 
 0.333333  0.250000  0.250000  0.166667 
 0.166667  0.583333  0.250000  0.000000 
 0.000000  0.916667  0.083333  0.000000 
 0.500000  0.333333  0.000000  0.166667 
 0.000000  0.583333  0.416667  0.000000 
 0.333333  0.416667  0.000000  0.250000 
 0.000000  0.250000  0.083333  0.666667 
 0.000000  0.500000  0.500000  0.000000 
 0.333333  0.000000  0.166667  0.500000 
 0.333333  0.416667  0.250000  0.000000 
 0.000000  0.500000  0.166667  0.333333 
 0.666667  0.000000  0.083333  0.250000 
 0.000000  0.833333  0.000000  0.166667 
 0.000000  0.583333  0.000000  0.416667 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.583333  0.416667 
 0.000000  0.750000  0.250000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif VDMBNCCMSHTSWVYACYGKC MEME-2 regular expression
--------------------------------------------------------------------------------
[CAG][ATG][AC][GCT][ACG][CG]C[AC][CG][CAT][TC][CG][TA][CAG][CT][AT]C[CT]G[GT][CG]
--------------------------------------------------------------------------------




Time  2.61 secs.

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


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

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
CHO1                             8.42e-04  610_[+1(3.43e-07)]_16_\
    [+1(7.37e-08)]_148
CHO2                             4.72e-03  353_[+1(4.16e-07)]_434
FAS1                             3.41e-05  94_[+1(3.29e-09)]_693
FAS2                             9.42e-08  566_[+1(4.16e-07)]_130_\
    [+2(4.56e-09)]_70
ACC1                             2.04e-06  82_[+1(1.88e-07)]_121_\
    [+2(2.60e-07)]_563
INO1                             2.18e-09  121_[-2(1.40e-07)]_140_\
    [+2(6.95e-08)]_65_[-2(1.17e-09)]_9_[+2(8.57e-08)]_116_[-2(7.72e-08)]_13_\
    [-1(2.24e-06)]_36_[-1(3.13e-08)]_55_[+1(1.72e-07)]_3_[+2(3.58e-07)]_77
OPI3                             2.07e-05  87_[+2(3.51e-05)]_180_\
    [+2(2.60e-07)]_33_[+2(4.17e-07)]_77_[+2(4.49e-07)]_42_[-2(2.39e-07)]_59_\
    [-1(2.44e-06)]_204
--------------------------------------------------------------------------------

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


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

CPU: Timothys-iMac.local

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