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MEME - Motif discovery tool
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MEME version 5.4.0 (Release date: Tue Mar 9 17:38:20 2021 -0800)

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.

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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= common/psp_test.s
CONTROL SEQUENCES= --none--
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
iYBL030C-1               1.0000   1083  iYBR008C                 1.0000   1180  
iYBR076W                 1.0000    401  iYBR208C                 1.0000    396  
iYCR021C                 1.0000    325  iYDL037C-0               1.0000    954  
iYDL037C-1               1.0000    922  iYDR300C                 1.0000    586  
iYDR338C                 1.0000    463  iYDR441C                 1.0000    570  
iYDR505C                 1.0000    508  iYEL012W                 1.0000    584  
iYER028C                 1.0000    676  iYER045C-0               1.0000    835  
iYER072W                 1.0000    844  iYFL005W                 1.0000    854  
iYGR035C                 1.0000    734  
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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 common/psp_test.s -oc results/meme50 -psp common/psp_test.psp -minsites 5 -dna -revcomp -minw 7 -maxw 12 -nostatus -searchsize 0 -mpi 

model:  mod=         zoops    nmotifs=         1    evt=           inf
objective function:           em=       E-value of product of p-values
                              starts=   E-value of product of p-values
strands: + -
width:  minw=            7    maxw=           12
nsites: minsites=        5    maxsites=       17    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=           11915    N=              17
sample: seed=            0    hsfrac=          0
        searchsize=  11915    norand=         no    csites=       1000
Letter frequencies in dataset:
A 0.317 C 0.183 G 0.183 T 0.317 
Background letter frequencies (from file dataset with add-one prior applied):
A 0.317 C 0.183 G 0.183 T 0.317 
Background model order: 0
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MOTIF GCTTATGTAA MEME-1	width =  10  sites =  16  llr = 146  E-value = 2.8e+006
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	Motif GCTTATGTAA MEME-1 Description
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Simplified        A  ::::911:8a
pos.-specific     C  :8:::21:1:
probability       G  a1:1:283::
matrix            T  :1a916181:

         bits    2.5 *         
                 2.2 *         
                 2.0 *         
                 1.7 * *      *
Relative         1.5 ***      *
Entropy          1.2 ***** *  *
(13.2 bits)      1.0 ***** ****
                 0.7 ***** ****
                 0.5 ***** ****
                 0.2 **********
                 0.0 ----------

Multilevel           GCTTATGTAA
consensus                   G  
sequence                       
                               
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	Motif GCTTATGTAA MEME-1 sites sorted by position p-value
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Sequence name            Strand  Start   P-value               Site 
-------------            ------  ----- ---------            ----------
iYFL005W                     +    480  1.97e-06 AACTACTTGC GCTTATGTAA GGTTCCTGTA
iYDR338C                     +    104  1.97e-06 AAATATGCTT GCTTATGTAA AAATACAATC
iYBR076W                     +    270  1.97e-06 GCGTAATCAA GCTTATGTAA ATGGCGTGTC
iYBR008C                     -    238  5.39e-06 AAGGATATTT GCTTAGGTAA GGAGCAATAA
iYDR300C                     +    144  8.98e-06 GCATTAGTTC GCTGATGTAA TTTTTCATTT
iYDL037C-1                   -    152  8.98e-06 TTTAAACTTT GCTTATGTCA AATTTAAATT
iYER072W                     -    674  1.83e-05 TTTACATGGG GCTTATATAA TCGTGTTTTG
iYDR505C                     -    423  2.32e-05 AACCCGCAAA GCTGACGGAA AAAGTATCGG
iYDR441C                     -    294  2.91e-05 CTCCGTATAA GGTTATGTAA TCGGAAGTCG
iYGR035C                     -    259  3.29e-05 TTGTGAAAAA GCTTAAGGAA AGCCGCGGAT
iYER028C                     +    580  4.47e-05 TTAAAATTAT GTTTAGGTAA TGAAAAAATA
iYBR208C                     +    180  5.16e-05 GAAAAAAAAA GCTTAGCTAA GAGAGCCTGA
iYBL030C-1                   -    278  5.84e-05 TTGTATGTGG GCTTATGGTA TGCCTGCAGG
iYDL037C-0                   -    338  6.52e-05 CCGATTCTAT GCTTACAGAA TAACCGATAC
iYER045C-0                   +    634  1.77e-04 GCCTTGTTCT GCTTACTTCA TGCAGAGGTA
iYCR021C                     +     72  2.00e-04 TTGTTGTTTT GTTTTTGTAA TTATAAATAA
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	Motif GCTTATGTAA MEME-1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
iYFL005W                            2e-06  479_[+1]_365
iYDR338C                            2e-06  103_[+1]_350
iYBR076W                            2e-06  269_[+1]_122
iYBR008C                          5.4e-06  237_[-1]_933
iYDR300C                            9e-06  143_[+1]_433
iYDL037C-1                          9e-06  151_[-1]_761
iYER072W                          1.8e-05  673_[-1]_161
iYDR505C                          2.3e-05  422_[-1]_76
iYDR441C                          2.9e-05  293_[-1]_267
iYGR035C                          3.3e-05  258_[-1]_466
iYER028C                          4.5e-05  579_[+1]_87
iYBR208C                          5.2e-05  179_[+1]_207
iYBL030C-1                        5.8e-05  277_[-1]_796
iYDL037C-0                        6.5e-05  337_[-1]_607
iYER045C-0                        0.00018  633_[+1]_192
iYCR021C                           0.0002  71_[+1]_244
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	Motif GCTTATGTAA MEME-1 in BLOCKS format
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BL   MOTIF GCTTATGTAA width=10 seqs=16
iYFL005W                 (  480) GCTTATGTAA  1 
iYDR338C                 (  104) GCTTATGTAA  1 
iYBR076W                 (  270) GCTTATGTAA  1 
iYBR008C                 (  238) GCTTAGGTAA  1 
iYDR300C                 (  144) GCTGATGTAA  1 
iYDL037C-1               (  152) GCTTATGTCA  1 
iYER072W                 (  674) GCTTATATAA  1 
iYDR505C                 (  423) GCTGACGGAA  1 
iYDR441C                 (  294) GGTTATGTAA  1 
iYGR035C                 (  259) GCTTAAGGAA  1 
iYER028C                 (  580) GTTTAGGTAA  1 
iYBR208C                 (  180) GCTTAGCTAA  1 
iYBL030C-1               (  278) GCTTATGGTA  1 
iYDL037C-0               (  338) GCTTACAGAA  1 
iYER045C-0               (  634) GCTTACTTCA  1 
iYCR021C                 (   72) GTTTTTGTAA  1 
//

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	Motif GCTTATGTAA MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 10 n= 11762 bayes= 10.035 E= 2.8e+006 
 -1064  -1064    245  -1064 
 -1064    215   -155   -134 
 -1064  -1064  -1064    166 
 -1064  -1064    -55    146 
   156  -1064  -1064   -234 
  -234      4      4     83 
  -134   -155    204   -234 
 -1064  -1064     45    124 
   136    -55  -1064   -234 
   166  -1064  -1064  -1064 
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	Motif GCTTATGTAA MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 10 nsites= 16 E= 2.8e+006 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.812500  0.062500  0.125000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.125000  0.875000 
 0.937500  0.000000  0.000000  0.062500 
 0.062500  0.187500  0.187500  0.562500 
 0.125000  0.062500  0.750000  0.062500 
 0.000000  0.000000  0.250000  0.750000 
 0.812500  0.125000  0.000000  0.062500 
 1.000000  0.000000  0.000000  0.000000 
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	Motif GCTTATGTAA MEME-1 regular expression
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GCTTATG[TG]AA
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Time  0.61 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
-------------            ----------------  -------------
iYBL030C-1                       1.18e-01  277_[-1(5.84e-05)]_796
iYBR008C                         1.25e-02  237_[-1(5.39e-06)]_933
iYBR076W                         1.54e-03  269_[+1(1.97e-06)]_122
iYBR208C                         3.91e-02  179_[+1(5.16e-05)]_207
iYCR021C                         1.19e-01  325
iYDL037C-0                       1.16e-01  337_[-1(6.52e-05)]_607
iYDL037C-1                       1.63e-02  151_[-1(8.98e-06)]_761
iYDR300C                         1.03e-02  143_[+1(8.98e-06)]_433
iYDR338C                         1.79e-03  103_[+1(1.97e-06)]_350
iYDR441C                         3.22e-02  293_[-1(2.91e-05)]_267
iYDR505C                         2.29e-02  422_[-1(2.32e-05)]_76
iYEL012W                         8.65e-01  584
iYER028C                         5.79e-02  579_[+1(4.47e-05)]_87
iYER045C-0                       2.54e-01  835
iYER072W                         3.01e-02  673_[-1(1.83e-05)]_161
iYFL005W                         3.33e-03  479_[+1(1.97e-06)]_365
iYGR035C                         4.66e-02  215_[+1(6.30e-05)]_33_\
    [-1(3.29e-05)]_466
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Stopped because requested number of motifs (1) found.
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CPU: Timothys-Mac-Mini.local

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