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********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.4 (Release date:    )

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme.nbcr.net.

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.nbcr.net.
********************************************************************************


********************************************************************************
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
********************************************************************************
DATAFILE= HEM4-HEM12.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YOR278W         1.0000    635  MIT_Spar_c261_21317      1.0000    635  
MIT_Smik_c492_20940      1.0000    635  WashU_Skud_Contig1682.4  1.0000    635  
WashU_Sbay_Contig635.57  1.0000    635  SGD_Scer_YDR047W         1.0000   1000  
MIT_Spar_c130_3923       1.0000   1000  MIT_Sbay_c896_21277      1.0000   1000  
WashU_Skud_Contig1362.1  1.0000    761  
********************************************************************************

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

command: meme HEM4-HEM12.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 

model:  mod=          oops    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            6    maxw=           20    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        9    maxsites=        9    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            6936    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.299 C 0.201 G 0.201 T 0.299 
Background letter frequencies (from yeast.nc.1.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
********************************************************************************


********************************************************************************
MOTIF  1	width =   20   sites =   9   llr = 188   E-value = 6.5e-019
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :9a4a:a::6::1:::1718
pos.-specific     C  21:::a::64a:684a9::2
probability       G  :::6::::4::a:::::21:
matrix            T  8::::::a::::326::18:

         bits    2.5      *    **   *    
                 2.3      *    **   *    
                 2.0      *    **   **   
                 1.8      *    **   **   
Information      1.5   * ***** ** * **   
content          1.3  ** ***** ** * **   
(30.1 bits)      1.0 ************ ****  *
                 0.8 ***************** **
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TAAGACATCACGCCTCCATA
consensus            C  A    GC  TTC  G C
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      -    370  3.48e-12 TTACCATGCT TAAGACATCACGCCTCCATA TGTCTATGTC
WashU_Skud_Contig1682.4      -    363  3.48e-12 TTACCATGCT TAAGACATCACGCCTCCATA TGTCTATGTA
MIT_Smik_c492_20940          -    368  3.48e-12 TTACCATGCT TAAGACATCACGCCTCCATA TGTCTATATA
MIT_Spar_c261_21317          -    362  3.48e-12 TTACCATGCT TAAGACATCACGCCTCCATA TGTCTATATA
SGD_Scer_YOR278W             -    359  3.48e-12 TTACCATGCT TAAGACATCACGCCTCCATA TGTCTATATA
MIT_Spar_c130_3923           +    644  1.59e-10 TGGCGCAATT CAAAACATGCCGTCCCCGTA CTAAGTTATG
SGD_Scer_YDR047W             +    646  4.90e-10 GCTGTGCATT TAAAACATGCCGTTCCCGTA CCAAGTTATA
WashU_Skud_Contig1362.1      +    646  3.58e-09 CTGGAACAAA TCAAACATGCCGTCCCCTAC CAGCTCTCGA
MIT_Sbay_c896_21277          +    650  9.08e-09 ATTGACAAGA CAAAACATGCCGATCCAAGC CAGGCGAAAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           3.5e-12  369_[-1]_246
WashU_Skud_Contig1682.4           3.5e-12  362_[-1]_253
MIT_Smik_c492_20940               3.5e-12  367_[-1]_248
MIT_Spar_c261_21317               3.5e-12  361_[-1]_254
SGD_Scer_YOR278W                  3.5e-12  358_[-1]_257
MIT_Spar_c130_3923                1.6e-10  643_[+1]_337
SGD_Scer_YDR047W                  4.9e-10  645_[+1]_335
WashU_Skud_Contig1362.1           3.6e-09  645_[+1]_96
MIT_Sbay_c896_21277               9.1e-09  649_[+1]_331
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
WashU_Sbay_Contig635.57  (  370) TAAGACATCACGCCTCCATA  1 
WashU_Skud_Contig1682.4  (  363) TAAGACATCACGCCTCCATA  1 
MIT_Smik_c492_20940      (  368) TAAGACATCACGCCTCCATA  1 
MIT_Spar_c261_21317      (  362) TAAGACATCACGCCTCCATA  1 
SGD_Scer_YOR278W         (  359) TAAGACATCACGCCTCCATA  1 
MIT_Spar_c130_3923       (  644) CAAAACATGCCGTCCCCGTA  1 
SGD_Scer_YDR047W         (  646) TAAAACATGCCGTTCCCGTA  1 
WashU_Skud_Contig1362.1  (  646) TCAAACATGCCGTCCCCTAC  1 
MIT_Sbay_c896_21277      (  650) CAAAACATGCCGATCCAAGC  1 
//

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

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6765 bayes= 9.55203 E= 6.5e-019 
  -982     34   -982    126 
   145    -66   -982   -982 
   162   -982   -982   -982 
    45   -982    166   -982 
   162   -982   -982   -982 
  -982    251   -982   -982 
   162   -982   -982   -982 
  -982   -982   -982    162 
  -982    166    134   -982 
    78    134   -982   -982 
  -982    251   -982   -982 
  -982   -982    251   -982 
  -154    166   -982      4 
  -982    215   -982    -55 
  -982    134   -982     78 
  -982    251   -982   -982 
  -154    234   -982   -982 
   104   -982     34   -154 
  -154   -982    -66    126 
   126     34   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.5e-019 
 0.000000  0.222222  0.000000  0.777778 
 0.888889  0.111111  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 1.000000  0.000000  0.000000  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  0.555556  0.444444  0.000000 
 0.555556  0.444444  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.111111  0.555556  0.000000  0.333333 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.444444  0.000000  0.555556 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.888889  0.000000  0.000000 
 0.666667  0.000000  0.222222  0.111111 
 0.111111  0.000000  0.111111  0.777778 
 0.777778  0.222222  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
[TC]AA[GA]ACAT[CG][AC]CG[CT][CT][TC]CC[AG]T[AC]
--------------------------------------------------------------------------------




Time  5.21 secs.

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


********************************************************************************
MOTIF  2	width =   20   sites =   9   llr = 180   E-value = 1.7e-016
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  ::1:7:::73:::3:::::9
pos.-specific     C  :188::aa2::::7:8::11
probability       G  1::128::1:1:a:a:112:
matrix            T  991112:::79a:::2997:

         bits    2.5       **    * *     
                 2.3       **    * *     
                 2.0       **    * *     
                 1.8       **    * *     
Information      1.5    * ***   ** **    
content          1.3 **** ***  ******** *
(28.8 bits)      1.0 **** ***  ******** *
                 0.8 **** ***************
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           TTCCAGCCATTTGCGCTTTA
consensus                GT  CA   A T  G 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig1682.4      +    335  6.64e-13 ATTGGTCTAC TTCCAGCCATTTGCGCTTTA CATAGACATA
MIT_Smik_c492_20940          +    340  6.64e-13 ATTTGTCTAC TTCCAGCCATTTGCGCTTTA TATAGACATA
MIT_Spar_c261_21317          +    334  6.64e-13 ATTGGTCTAC TTCCAGCCATTTGCGCTTTA TATAGACATA
SGD_Scer_YOR278W             +    331  6.64e-13 ATTGGTCTAC TTCCAGCCATTTGCGCTTTA TATAGACATA
WashU_Sbay_Contig635.57      +    342  1.74e-12 ATTGGTCTAC TTCCAGCCATTTGCGCTTGA CATAGACATA
MIT_Spar_c130_3923           +    720  2.83e-09 AATGCTGCCG TTCCGTCCCATTGAGTTTTA TTTTCCTTCT
SGD_Scer_YDR047W             +    720  2.83e-09 AATGCTGCCG TTCCGTCCCATTGAGTTTTA TTTTCCTTCT
MIT_Sbay_c896_21277          +    833  4.51e-08 AAGGTCAGTT TTATAGCCGTGTGCGCGGCA TCGAGAGACA
WashU_Skud_Contig1362.1      -     39  7.81e-08 TTTTTTTAGA GCTGTGCCAATTGAGCTTGC TACCAATCTA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1682.4           6.6e-13  334_[+2]_281
MIT_Smik_c492_20940               6.6e-13  339_[+2]_276
MIT_Spar_c261_21317               6.6e-13  333_[+2]_282
SGD_Scer_YOR278W                  6.6e-13  330_[+2]_285
WashU_Sbay_Contig635.57           1.7e-12  341_[+2]_274
MIT_Spar_c130_3923                2.8e-09  719_[+2]_261
SGD_Scer_YDR047W                  2.8e-09  719_[+2]_261
MIT_Sbay_c896_21277               4.5e-08  832_[+2]_148
WashU_Skud_Contig1362.1           7.8e-08  38_[-2]_703
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=9
WashU_Skud_Contig1682.4  (  335) TTCCAGCCATTTGCGCTTTA  1 
MIT_Smik_c492_20940      (  340) TTCCAGCCATTTGCGCTTTA  1 
MIT_Spar_c261_21317      (  334) TTCCAGCCATTTGCGCTTTA  1 
SGD_Scer_YOR278W         (  331) TTCCAGCCATTTGCGCTTTA  1 
WashU_Sbay_Contig635.57  (  342) TTCCAGCCATTTGCGCTTGA  1 
MIT_Spar_c130_3923       (  720) TTCCGTCCCATTGAGTTTTA  1 
SGD_Scer_YDR047W         (  720) TTCCGTCCCATTGAGTTTTA  1 
MIT_Sbay_c896_21277      (  833) TTATAGCCGTGTGCGCGGCA  1 
WashU_Skud_Contig1362.1  (   39) GCTGTGCCAATTGAGCTTGC  1 
//

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

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6765 bayes= 9.55203 E= 1.7e-016 
  -982   -982    -66    145 
  -982    -66   -982    145 
  -154    215   -982   -154 
  -982    215    -66   -154 
   104   -982     34   -154 
  -982   -982    215    -55 
  -982    251   -982   -982 
  -982    251   -982   -982 
   104     34    -66   -982 
     4   -982   -982    104 
  -982   -982    -66    145 
  -982   -982   -982    162 
  -982   -982    251   -982 
     4    192   -982   -982 
  -982   -982    251   -982 
  -982    215   -982    -55 
  -982   -982    -66    145 
  -982   -982    -66    145 
  -982    -66     34    104 
   145    -66   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.7e-016 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  0.111111  0.000000  0.888889 
 0.111111  0.777778  0.000000  0.111111 
 0.000000  0.777778  0.111111  0.111111 
 0.666667  0.000000  0.222222  0.111111 
 0.000000  0.000000  0.777778  0.222222 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.666667  0.222222  0.111111  0.000000 
 0.333333  0.000000  0.000000  0.666667 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.333333  0.666667  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  0.111111  0.222222  0.666667 
 0.888889  0.111111  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
TTCC[AG][GT]CC[AC][TA]TTG[CA]G[CT]TT[TG]A
--------------------------------------------------------------------------------




Time 10.37 secs.

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


********************************************************************************
MOTIF  3	width =   15   sites =   9   llr = 143   E-value = 1.2e-009
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  8::::1a9:9::9::
pos.-specific     C  ::a62:::1::a:21
probability       G  13::89:1911::8:
matrix            T  17:4::::::9:1:9

         bits    2.5   *        *   
                 2.3   *        *   
                 2.0   *  *  *  *   
                 1.8   * **  *  * * 
Information      1.5   * *** *  * * 
content          1.3   * ******** **
(22.9 bits)      1.0  **************
                 0.8 ***************
                 0.5 ***************
                 0.3 ***************
                 0.0 ---------------

Multilevel           ATCCGGAAGATCAGT
consensus             G TC        C 
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Sbay_Contig635.57      +    399  6.31e-10 AAGCATGGTA ATCCGGAAGATCAGT TTATTGAATG
WashU_Skud_Contig1682.4      +    392  6.31e-10 AAGCATGGTA ATCCGGAAGATCAGT TTATTGAATG
MIT_Smik_c492_20940          +    397  6.31e-10 AAGCATGGTA ATCCGGAAGATCAGT TTATTGAATG
MIT_Spar_c261_21317          +    391  6.31e-10 AAGCATGGTA ATCCGGAAGATCAGT TTATTGAATG
SGD_Scer_YOR278W             +    388  6.31e-10 AAGCATGGTA ATCCGGAAGATCAGT TTATTGAATG
MIT_Sbay_c896_21277          +    817  1.82e-07 CATCTCGCTA AGCTGAAAGGTCAGT TTTATAGCCG
MIT_Spar_c130_3923           -    922  1.82e-07 CGTTGATCGC AGCTCGAGGATCAGC TAGTGAAATA
SGD_Scer_YDR047W             +    134  2.44e-07 TGTTACCTTC GTCTGGAACATCACT AATTCGAGCG
WashU_Skud_Contig1362.1      +    363  9.95e-07 AATTTGCTAA TGCTCGAAGAGCTCT CAATCAATCA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           6.3e-10  398_[+3]_222
WashU_Skud_Contig1682.4           6.3e-10  391_[+3]_229
MIT_Smik_c492_20940               6.3e-10  396_[+3]_224
MIT_Spar_c261_21317               6.3e-10  390_[+3]_230
SGD_Scer_YOR278W                  6.3e-10  387_[+3]_233
MIT_Sbay_c896_21277               1.8e-07  816_[+3]_169
MIT_Spar_c130_3923                1.8e-07  921_[-3]_64
SGD_Scer_YDR047W                  2.4e-07  133_[+3]_852
WashU_Skud_Contig1362.1             1e-06  362_[+3]_384
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=15 seqs=9
WashU_Sbay_Contig635.57  (  399) ATCCGGAAGATCAGT  1 
WashU_Skud_Contig1682.4  (  392) ATCCGGAAGATCAGT  1 
MIT_Smik_c492_20940      (  397) ATCCGGAAGATCAGT  1 
MIT_Spar_c261_21317      (  391) ATCCGGAAGATCAGT  1 
SGD_Scer_YOR278W         (  388) ATCCGGAAGATCAGT  1 
MIT_Sbay_c896_21277      (  817) AGCTGAAAGGTCAGT  1 
MIT_Spar_c130_3923       (  922) AGCTCGAGGATCAGC  1 
SGD_Scer_YDR047W         (  134) GTCTGGAACATCACT  1 
WashU_Skud_Contig1362.1  (  363) TGCTCGAAGAGCTCT  1 
//

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

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 6810 bayes= 9.56161 E= 1.2e-009 
   126   -982    -66   -154 
  -982   -982     92    104 
  -982    251   -982   -982 
  -982    166   -982     45 
  -982     34    215   -982 
  -154   -982    234   -982 
   162   -982   -982   -982 
   145   -982    -66   -982 
  -982    -66    234   -982 
   145   -982    -66   -982 
  -982   -982    -66    145 
  -982    251   -982   -982 
   145   -982   -982   -154 
  -982     34    215   -982 
  -982    -66   -982    145 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 1.2e-009 
 0.777778  0.000000  0.111111  0.111111 
 0.000000  0.000000  0.333333  0.666667 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.555556  0.000000  0.444444 
 0.000000  0.222222  0.777778  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.111111  0.888889  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  1.000000  0.000000  0.000000 
 0.888889  0.000000  0.000000  0.111111 
 0.000000  0.222222  0.777778  0.000000 
 0.000000  0.111111  0.000000  0.888889 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
A[TG]C[CT][GC]GAAGATCA[GC]T
--------------------------------------------------------------------------------




Time 15.31 secs.

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


********************************************************************************
MOTIF  4	width =   20   sites =   9   llr = 174   E-value = 1.7e-013
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  ::::6:::::4::a:3:93:
pos.-specific     C  1911::4:a:486:248:46
probability       G  ::::4a6a:::::::11:23
matrix            T  9199:::::a124:8111:1

         bits    2.5      * **           
                 2.3      * **           
                 2.0  *   * **           
                 1.8  *   * **           
Information      1.5  *   ***** * *  *   
content          1.3 **** ***** * *  *   
(27.9 bits)      1.0 ********** **** ** *
                 0.8 ********** **** ****
                 0.5 *************** ****
                 0.3 ********************
                 0.0 --------------------

Multilevel           TCTTAGGGCTACCATCCACC
consensus                G C   CTT CA  AG
sequence                               G 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c261_21317          +    548  3.46e-12 TTCGTTTTTC TCTTAGGGCTCCCATCCAAC TGTCGGCGAG
WashU_Sbay_Contig635.57      +    555  1.43e-11 TTTCTCTTTT TCTTAGGGCTCCTATCCAGC TGCCTGCGAA
MIT_Spar_c130_3923           -    287  2.21e-11 TTATTCGCTA TCTTGGCGCTACCATACACG ATTTTTTTTC
SGD_Scer_YDR047W             -    289  3.04e-10 TTATCCGCCA TCTTGGCGCTATCATACACG ATCTTTTTCA
MIT_Smik_c492_20940          +    546  5.86e-10 TTTCGCTTTT TCTTAGGGCTCCTATCTAAC TCTCGGGCGA
WashU_Skud_Contig1362.1      -    246  1.17e-09 TGCCCGTTTT CCTTGGCGCTACCATACACT TCCTCTGTTT
MIT_Sbay_c896_21277          -    239  5.15e-09 TATCTGCCTT TTCTGGCGCTACCATGCAGC TTCCTCGTTT
WashU_Skud_Contig1682.4      +    542  1.02e-08 TTTCACTTTT TCTCAGGGCTTTTACCCAAC TGCCGACAAA
SGD_Scer_YOR278W             +    531  1.19e-08 TCGCTTTATC TCTTAGGGCTCCTACTGTCG GTAGAGAAAA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c261_21317               3.5e-12  547_[+4]_68
WashU_Sbay_Contig635.57           1.4e-11  554_[+4]_61
MIT_Spar_c130_3923                2.2e-11  286_[-4]_694
SGD_Scer_YDR047W                    3e-10  288_[-4]_692
MIT_Smik_c492_20940               5.9e-10  545_[+4]_70
WashU_Skud_Contig1362.1           1.2e-09  245_[-4]_496
MIT_Sbay_c896_21277               5.2e-09  238_[-4]_742
WashU_Skud_Contig1682.4             1e-08  541_[+4]_74
SGD_Scer_YOR278W                  1.2e-08  530_[+4]_85
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=9
MIT_Spar_c261_21317      (  548) TCTTAGGGCTCCCATCCAAC  1 
WashU_Sbay_Contig635.57  (  555) TCTTAGGGCTCCTATCCAGC  1 
MIT_Spar_c130_3923       (  287) TCTTGGCGCTACCATACACG  1 
SGD_Scer_YDR047W         (  289) TCTTGGCGCTATCATACACG  1 
MIT_Smik_c492_20940      (  546) TCTTAGGGCTCCTATCTAAC  1 
WashU_Skud_Contig1362.1  (  246) CCTTGGCGCTACCATACACT  1 
MIT_Sbay_c896_21277      (  239) TTCTGGCGCTACCATGCAGC  1 
WashU_Skud_Contig1682.4  (  542) TCTCAGGGCTTTTACCCAAC  1 
SGD_Scer_YOR278W         (  531) TCTTAGGGCTCCTACTGTCG  1 
//

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

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6765 bayes= 9.55203 E= 1.7e-013 
  -982    -66   -982    145 
  -982    234   -982   -154 
  -982    -66   -982    145 
  -982    -66   -982    145 
    78   -982    134   -982 
  -982   -982    251   -982 
  -982    134    166   -982 
  -982   -982    251   -982 
  -982    251   -982   -982 
  -982   -982   -982    162 
    45    134   -982   -154 
  -982    215   -982    -55 
  -982    166   -982     45 
   162   -982   -982   -982 
  -982     34   -982    126 
     4    134    -66   -154 
  -982    215    -66   -154 
   145   -982   -982   -154 
     4    134     34   -982 
  -982    166     92   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.7e-013 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.111111  0.000000  0.888889 
 0.555556  0.000000  0.444444  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.444444  0.555556  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.444444  0.444444  0.000000  0.111111 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.555556  0.000000  0.444444 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.222222  0.000000  0.777778 
 0.333333  0.444444  0.111111  0.111111 
 0.000000  0.777778  0.111111  0.111111 
 0.888889  0.000000  0.000000  0.111111 
 0.333333  0.444444  0.222222  0.000000 
 0.000000  0.555556  0.333333  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
TCTT[AG]G[GC]GCT[AC][CT][CT]A[TC][CA]CA[CAG][CG]
--------------------------------------------------------------------------------




Time 20.21 secs.

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


********************************************************************************
MOTIF  5	width =   20   sites =   9   llr = 167   E-value = 1.7e-011
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  921:9181:18181::881:
pos.-specific     C  :1:118:99:2:118:1:98
probability       G  ::9:::1::::9:61a12:2
matrix            T  17:9:11:19::121:::::

         bits    2.5                *    
                 2.3                *    
                 2.0   *    **  *   *  * 
                 1.8   *    **  *   *  **
Information      1.5   *    **  *  **  **
content          1.3   **** **  *  **  **
(26.7 bits)      1.0 * **** *****  ** ***
                 0.8 * *********** ******
                 0.5 ********************
                 0.3 ********************
                 0.0 --------------------

Multilevel           ATGTACACCTAGAGCGAACC
consensus             A        C  T   G G
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      +    232  3.60e-13 TAAAAAAAAC ATGTACACCTAGAGCGAACC AGTGATAATT
WashU_Skud_Contig1682.4      +    226  3.60e-13 AAGTAGAGAT ATGTACACCTAGAGCGAACC AATGATAATT
MIT_Smik_c492_20940          +    229  3.60e-13 AAGTGAAGAT ATGTACACCTAGAGCGAACC AATAATAATT
MIT_Spar_c261_21317          +    224  3.60e-13 CAAAATGAAT ATGTACACCTAGAGCGAACC AATGATAATT
SGD_Scer_YOR278W             +    220  3.60e-13 AAGTGAAGAT ATGTACACCTAGAGCGAACC AATGATAATT
SGD_Scer_YDR047W             +    449  2.13e-07 TCGCAGTGCT ACGTACGCCAAAAACGCGCG CATGGAAGTA
MIT_Sbay_c896_21277          +    384  2.80e-07 GCTTGGTAAC AAATAAACCTAGCCGGGGCC AGAATTTCAC
MIT_Spar_c130_3923           +    120  3.31e-07 TATTTACTCT ATGTCCACTTCGTTTGAAAC ATCAGTGGTT
WashU_Skud_Contig1362.1      +    684  7.95e-07 GAAGCGGGCC TAGCATTACTCGATCGAACG TTGCCGTTTA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           3.6e-13  231_[+5]_384
WashU_Skud_Contig1682.4           3.6e-13  225_[+5]_390
MIT_Smik_c492_20940               3.6e-13  228_[+5]_387
MIT_Spar_c261_21317               3.6e-13  223_[+5]_392
SGD_Scer_YOR278W                  3.6e-13  219_[+5]_396
SGD_Scer_YDR047W                  2.1e-07  448_[+5]_532
MIT_Sbay_c896_21277               2.8e-07  383_[+5]_597
MIT_Spar_c130_3923                3.3e-07  119_[+5]_861
WashU_Skud_Contig1362.1             8e-07  683_[+5]_58
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=9
WashU_Sbay_Contig635.57  (  232) ATGTACACCTAGAGCGAACC  1 
WashU_Skud_Contig1682.4  (  226) ATGTACACCTAGAGCGAACC  1 
MIT_Smik_c492_20940      (  229) ATGTACACCTAGAGCGAACC  1 
MIT_Spar_c261_21317      (  224) ATGTACACCTAGAGCGAACC  1 
SGD_Scer_YOR278W         (  220) ATGTACACCTAGAGCGAACC  1 
SGD_Scer_YDR047W         (  449) ACGTACGCCAAAAACGCGCG  1 
MIT_Sbay_c896_21277      (  384) AAATAAACCTAGCCGGGGCC  1 
MIT_Spar_c130_3923       (  120) ATGTCCACTTCGTTTGAAAC  1 
WashU_Skud_Contig1362.1  (  684) TAGCATTACTCGATCGAACG  1 
//

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

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 6765 bayes= 9.55203 E= 1.7e-011 
   145   -982   -982   -154 
   -55    -66   -982    104 
  -154   -982    234   -982 
  -982    -66   -982    145 
   145    -66   -982   -982 
  -154    215   -982   -154 
   126   -982    -66   -154 
  -154    234   -982   -982 
  -982    234   -982   -154 
  -154   -982   -982    145 
   126     34   -982   -982 
  -154   -982    234   -982 
   126    -66   -982   -154 
  -154    -66    166    -55 
  -982    215    -66   -154 
  -982   -982    251   -982 
   126    -66    -66   -982 
   126   -982     34   -982 
  -154    234   -982   -982 
  -982    215     34   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.7e-011 
 0.888889  0.000000  0.000000  0.111111 
 0.222222  0.111111  0.000000  0.666667 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.888889  0.111111  0.000000  0.000000 
 0.111111  0.777778  0.000000  0.111111 
 0.777778  0.000000  0.111111  0.111111 
 0.111111  0.888889  0.000000  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.111111  0.000000  0.000000  0.888889 
 0.777778  0.222222  0.000000  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.777778  0.111111  0.000000  0.111111 
 0.111111  0.111111  0.555556  0.222222 
 0.000000  0.777778  0.111111  0.111111 
 0.000000  0.000000  1.000000  0.000000 
 0.777778  0.111111  0.111111  0.000000 
 0.777778  0.000000  0.222222  0.000000 
 0.111111  0.888889  0.000000  0.000000 
 0.000000  0.777778  0.222222  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
A[TA]GTACACCT[AC]GA[GT]CGA[AG]C[CG]
--------------------------------------------------------------------------------




Time 25.01 secs.

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


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

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YOR278W                 4.46e-32  [-5(9.93e-05)]_199_[+5(3.60e-13)]_91_[+2(6.64e-13)]_8_[-1(3.48e-12)]_9_[+3(6.31e-10)]_128_[+4(1.19e-08)]_85
MIT_Spar_c261_21317              1.84e-35  25_[+4(3.48e-05)]_54_[+1(1.15e-05)]_104_[+5(3.60e-13)]_90_[+2(6.64e-13)]_8_[-1(3.48e-12)]_9_[+3(6.31e-10)]_142_[+4(3.46e-12)]_68
MIT_Smik_c492_20940              2.51e-33  228_[+5(3.60e-13)]_91_[+2(6.64e-13)]_8_[-1(3.48e-12)]_9_[+3(6.31e-10)]_134_[+4(5.86e-10)]_70
WashU_Skud_Contig1682.4          3.86e-32  225_[+5(3.60e-13)]_89_[+2(6.64e-13)]_8_[-1(3.48e-12)]_9_[+3(6.31e-10)]_135_[+4(1.02e-08)]_74
WashU_Sbay_Contig635.57          1.81e-34  231_[+5(3.60e-13)]_90_[+2(1.74e-12)]_8_[-1(3.48e-12)]_9_[+3(6.31e-10)]_141_[+4(1.43e-11)]_61
SGD_Scer_YDR047W                 2.76e-19  133_[+3(2.44e-07)]_140_[-4(3.04e-10)]_140_[+5(2.13e-07)]_177_[+1(4.90e-10)]_54_[+2(2.83e-09)]_61_[-1(8.87e-05)]_22_[+3(5.89e-06)]_55_[-3(5.20e-05)]_73
MIT_Spar_c130_3923               9.70e-21  42_[+3(1.33e-05)]_62_[+5(3.31e-07)]_147_[-4(2.21e-11)]_337_[+1(1.59e-10)]_56_[+2(2.83e-09)]_38_[-5(5.60e-05)]_13_[-1(8.87e-05)]_55_[-3(2.21e-05)]_21_[-3(1.82e-07)]_64
MIT_Sbay_c896_21277              7.11e-16  118_[+3(1.87e-05)]_105_[-4(5.15e-09)]_125_[+5(2.80e-07)]_138_[-2(1.57e-05)]_88_[+1(9.08e-09)]_45_[+2(1.89e-05)]_17_[+4(7.61e-05)]_45_[+3(1.82e-07)]_1_[+2(4.51e-08)]_148
WashU_Skud_Contig1362.1          4.40e-16  38_[-2(7.81e-08)]_187_[-4(1.17e-09)]_97_[+3(9.95e-07)]_268_[+1(3.58e-09)]_18_[+5(7.95e-07)]_58
--------------------------------------------------------------------------------

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


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: dhn02990.mrc-dunn.cam.ac.uk

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