The Perl Toolchain Summit needs more sponsors. If your company depends on Perl, please support this very important event.
********************************************************************************
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= HEM2-HEM12.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YGL040C         1.0000   1000  MIT_Spar_c19_8512        1.0000   1000  
MIT_Smik_c273_7756       1.0000   1000  MIT_Sbay_c77_8808        1.0000   1000  
WashU_Skud_Contig2052.17 1.0000   1000  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 HEM2-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=            8761    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.309 C 0.191 G 0.191 T 0.309 
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 = 201   E-value = 6.7e-025
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  ::2711:1aa1:a32::a::
pos.-specific     C  a272::a7:::9:66:a:99
probability       G  :11199:2::21:12a::1:
matrix            T  :7::::::::7::::::::1

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

Multilevel           CTCAGGCCAATCACCGCACC
consensus             CAC   G  G  AA     
sequence                           G     
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2052.17     +    179  5.70e-14 GGCAGCTTGC CTCAGGCCAATCACCGCACC GAACAGGGAT
MIT_Smik_c273_7756           +    178  5.70e-14 TGTATGTTGC CTCAGGCCAATCACCGCACC GAATAAGGAT
MIT_Spar_c19_8512            +    180  5.70e-14 GGCAGCTTGC CTCAGGCCAATCACCGCACC GAACAGGGAT
MIT_Sbay_c77_8808            +    180  4.81e-13 GGCAGCCTGC CGCAGGCCAATCACCGCACC GCCCGGAGAT
SGD_Scer_YGL040C             +    179  4.85e-12 GGAAGCTTGC CTCAAGCCAATCACCGCACC GAACAGGGAT
SGD_Scer_YDR047W             +    616  4.68e-10 CTTTAACAAT CCACGGCGAAACAAGGCACC GCTGTGCATT
MIT_Spar_c130_3923           +    612  4.99e-10 TTTTTACAAA CTACGGCAAAGCAAAGCACC ACTGGCGCAA
MIT_Sbay_c896_21277          +    896  5.96e-10 AATTCTCGAG CTGAGGCCAATGAAGGCAGC TTCCAGGGCT
WashU_Skud_Contig1362.1      +    614  4.38e-09 ATTTTACAAA CCCGGACGAAGCAGAGCACT TGCTGGAACA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2052.17          5.7e-14  178_[+1]_802
MIT_Smik_c273_7756                5.7e-14  177_[+1]_803
MIT_Spar_c19_8512                 5.7e-14  179_[+1]_801
MIT_Sbay_c77_8808                 4.8e-13  179_[+1]_801
SGD_Scer_YGL040C                  4.9e-12  178_[+1]_802
SGD_Scer_YDR047W                  4.7e-10  615_[+1]_365
MIT_Spar_c130_3923                  5e-10  611_[+1]_369
MIT_Sbay_c896_21277                 6e-10  895_[+1]_85
WashU_Skud_Contig1362.1           4.4e-09  613_[+1]_128
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
WashU_Skud_Contig2052.17 (  179) CTCAGGCCAATCACCGCACC  1 
MIT_Smik_c273_7756       (  178) CTCAGGCCAATCACCGCACC  1 
MIT_Spar_c19_8512        (  180) CTCAGGCCAATCACCGCACC  1 
MIT_Sbay_c77_8808        (  180) CGCAGGCCAATCACCGCACC  1 
SGD_Scer_YGL040C         (  179) CTCAAGCCAATCACCGCACC  1 
SGD_Scer_YDR047W         (  616) CCACGGCGAAACAAGGCACC  1 
MIT_Spar_c130_3923       (  612) CTACGGCAAAGCAAAGCACC  1 
MIT_Sbay_c896_21277      (  896) CTGAGGCCAATGAAGGCAGC  1 
WashU_Skud_Contig1362.1  (  614) CCCGGACGAAGCAGAGCACT  1 
//

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

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8590 bayes= 9.89701 E= 6.7e-025 
  -982    251   -982   -982 
  -982     34    -66    104 
   -55    192    -66   -982 
   104     34    -66   -982 
  -154   -982    234   -982 
  -154   -982    234   -982 
  -982    251   -982   -982 
  -154    192     34   -982 
   162   -982   -982   -982 
   162   -982   -982   -982 
  -154   -982     34    104 
  -982    234    -66   -982 
   162   -982   -982   -982 
     4    166    -66   -982 
   -55    166     34   -982 
  -982   -982    251   -982 
  -982    251   -982   -982 
   162   -982   -982   -982 
  -982    234    -66   -982 
  -982    234   -982   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.7e-025 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.222222  0.111111  0.666667 
 0.222222  0.666667  0.111111  0.000000 
 0.666667  0.222222  0.111111  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.666667  0.222222  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.111111  0.000000  0.222222  0.666667 
 0.000000  0.888889  0.111111  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.333333  0.555556  0.111111  0.000000 
 0.222222  0.555556  0.222222  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.888889  0.111111  0.000000 
 0.000000  0.888889  0.000000  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
C[TC][CA][AC]GGC[CG]AA[TG]CA[CA][CAG]GCACC
--------------------------------------------------------------------------------




Time  8.20 secs.

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


********************************************************************************
MOTIF  2	width =   20   sites =   9   llr = 174   E-value = 1.0e-012
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  8:82:391:1:::::::9::
pos.-specific     C  27122::::1a17:::1:7a
probability       G  ::16761::8::3a13::3:
matrix            T  :3::11:9a::9::9791::

         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           ACAGGGATTGCTCGTTTACC
consensus            CT ACA      G  G  G 
sequence                C                
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig2052.17     +    201  3.60e-13 ACCGCACCGA ACAGGGATTGCTCGTTTACC CGTTGCGTTC
MIT_Spar_c19_8512            +    202  3.60e-13 ACCGCACCGA ACAGGGATTGCTCGTTTACC CGTAGTTTGA
SGD_Scer_YGL040C             +    201  3.60e-13 ACCGCACCGA ACAGGGATTGCTCGTTTACC CGTATTTTGA
MIT_Smik_c273_7756           +    200  6.88e-11 ACCGCACCGA ATAAGGATTGCTCGTTTACC CGTTGTTCGA
SGD_Scer_YDR047W             +    557  2.56e-09 TGATCCGAAG ACACCAATTGCTGGTGCAGC ATAGGAATAT
MIT_Sbay_c77_8808            +    201  4.15e-09 CACCGCACCG CCCGGAGATGCTCGTTTACC GTTGTGCACC
MIT_Sbay_c896_21277          -     39  1.46e-08 TCTTTGCTAA ATAGTGATTCCTGGGGTAGC TATTAGAATA
MIT_Spar_c130_3923           +    554  1.46e-08 ATGGTCAATG ACGCCAATTACTGGTGTAGC ATGAGAATAC
WashU_Skud_Contig1362.1      -    264  2.12e-08 GTCATTCTTT CTAAGTATTGCCCGTTTTCC TTGGCGCTAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig2052.17          3.6e-13  200_[+2]_780
MIT_Spar_c19_8512                 3.6e-13  201_[+2]_779
SGD_Scer_YGL040C                  3.6e-13  200_[+2]_780
MIT_Smik_c273_7756                6.9e-11  199_[+2]_781
SGD_Scer_YDR047W                  2.6e-09  556_[+2]_424
MIT_Sbay_c77_8808                 4.1e-09  200_[+2]_780
MIT_Sbay_c896_21277               1.5e-08  38_[-2]_942
MIT_Spar_c130_3923                1.5e-08  553_[+2]_427
WashU_Skud_Contig1362.1           2.1e-08  263_[-2]_478
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=9
WashU_Skud_Contig2052.17 (  201) ACAGGGATTGCTCGTTTACC  1 
MIT_Spar_c19_8512        (  202) ACAGGGATTGCTCGTTTACC  1 
SGD_Scer_YGL040C         (  201) ACAGGGATTGCTCGTTTACC  1 
MIT_Smik_c273_7756       (  200) ATAAGGATTGCTCGTTTACC  1 
SGD_Scer_YDR047W         (  557) ACACCAATTGCTGGTGCAGC  1 
MIT_Sbay_c77_8808        (  201) CCCGGAGATGCTCGTTTACC  1 
MIT_Sbay_c896_21277      (   39) ATAGTGATTCCTGGGGTAGC  1 
MIT_Spar_c130_3923       (  554) ACGCCAATTACTGGTGTAGC  1 
WashU_Skud_Contig1362.1  (  264) CTAAGTATTGCCCGTTTTCC  1 
//

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

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8590 bayes= 9.89701 E= 1.0e-012 
   126     34   -982   -982 
  -982    192   -982      4 
   126    -66    -66   -982 
   -55     34    166   -982 
  -982     34    192   -154 
     4   -982    166   -154 
   145   -982    -66   -982 
  -154   -982   -982    145 
  -982   -982   -982    162 
  -154    -66    215   -982 
  -982    251   -982   -982 
  -982    -66   -982    145 
  -982    192     92   -982 
  -982   -982    251   -982 
  -982   -982    -66    145 
  -982   -982     92    104 
  -982    -66   -982    145 
   145   -982   -982   -154 
  -982    192     92   -982 
  -982    251   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.0e-012 
 0.777778  0.222222  0.000000  0.000000 
 0.000000  0.666667  0.000000  0.333333 
 0.777778  0.111111  0.111111  0.000000 
 0.222222  0.222222  0.555556  0.000000 
 0.000000  0.222222  0.666667  0.111111 
 0.333333  0.000000  0.555556  0.111111 
 0.888889  0.000000  0.111111  0.000000 
 0.111111  0.000000  0.000000  0.888889 
 0.000000  0.000000  0.000000  1.000000 
 0.111111  0.111111  0.777778  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.666667  0.333333  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.111111  0.888889 
 0.000000  0.000000  0.333333  0.666667 
 0.000000  0.111111  0.000000  0.888889 
 0.888889  0.000000  0.000000  0.111111 
 0.000000  0.666667  0.333333  0.000000 
 0.000000  1.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
[AC][CT]A[GAC][GC][GA]ATTGCT[CG]GT[TG]TA[CG]C
--------------------------------------------------------------------------------




Time 16.04 secs.

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


********************************************************************************
MOTIF  3	width =   20   sites =   9   llr = 159   E-value = 7.4e-007
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :::23:16:::9:a784:9:
pos.-specific     C  a73623641::::::16:::
probability       G  ::7:2:3::4:11::1:a19
matrix            T  :3:227::96a:9:3::::1

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

Multilevel           CCGCATCATTTATAAACGAG
consensus             TCACCGC G    T A   
sequence                TG               
                         T               
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Sbay_c896_21277          +    216  1.03e-10 TCAAAAAACC CCGAACCCTGTATAAACGAG GAAGCTGCAT
MIT_Spar_c19_8512            -    151  6.18e-10 GGCAAGCTGC CCGCTTGATTTATAAAAGAG TAAGGCAACC
SGD_Scer_YDR047W             +    253  7.00e-10 AAACCCCGAA CCCTGTCCTGTATATACGAG AAACATTGAA
MIT_Sbay_c77_8808            -    155  1.63e-09 CTGCGGCAGG CTGCCTGATTTATAAAAGAG CAAGGCAACA
SGD_Scer_YGL040C             -    150  1.63e-09 GGCAAGCTTC CCGCTTGATTTATATAAGAG TAAGGCAACC
MIT_Spar_c130_3923           +    250  4.40e-09 AAACCCCGAA CCCTGTCCCGTATATACGAG GAACATTGAA
WashU_Skud_Contig1362.1      +    211  8.03e-09 CCAAAAAACC CCGAATCATGTAGAAGCGAG AAGTAAAACA
WashU_Skud_Contig2052.17     -    150  1.10e-08 GGCAAGCTGC CTGCCCAATTTATAAAAGAG AAAGGCAACT
MIT_Smik_c273_7756           +    871  1.32e-07 GAGTCATCAT CTCCACCCTTTGTAACCGGT GTCCTGCTCA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Sbay_c896_21277                 1e-10  215_[+3]_765
MIT_Spar_c19_8512                 6.2e-10  150_[-3]_830
SGD_Scer_YDR047W                    7e-10  252_[+3]_728
MIT_Sbay_c77_8808                 1.6e-09  154_[-3]_826
SGD_Scer_YGL040C                  1.6e-09  149_[-3]_831
MIT_Spar_c130_3923                4.4e-09  249_[+3]_731
WashU_Skud_Contig1362.1             8e-09  210_[+3]_531
WashU_Skud_Contig2052.17          1.1e-08  149_[-3]_831
MIT_Smik_c273_7756                1.3e-07  870_[+3]_110
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=9
MIT_Sbay_c896_21277      (  216) CCGAACCCTGTATAAACGAG  1 
MIT_Spar_c19_8512        (  151) CCGCTTGATTTATAAAAGAG  1 
SGD_Scer_YDR047W         (  253) CCCTGTCCTGTATATACGAG  1 
MIT_Sbay_c77_8808        (  155) CTGCCTGATTTATAAAAGAG  1 
SGD_Scer_YGL040C         (  150) CCGCTTGATTTATATAAGAG  1 
MIT_Spar_c130_3923       (  250) CCCTGTCCCGTATATACGAG  1 
WashU_Skud_Contig1362.1  (  211) CCGAATCATGTAGAAGCGAG  1 
WashU_Skud_Contig2052.17 (  150) CTGCCCAATTTATAAAAGAG  1 
MIT_Smik_c273_7756       (  871) CTCCACCCTTTGTAACCGGT  1 
//

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

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8590 bayes= 9.89701 E= 7.4e-007 
  -982    251   -982   -982 
  -982    192   -982      4 
  -982     92    192   -982 
   -55    166   -982    -55 
     4     34     34    -55 
  -982     92   -982    104 
  -154    166     92   -982 
    78    134   -982   -982 
  -982    -66   -982    145 
  -982   -982    134     78 
  -982   -982   -982    162 
   145   -982    -66   -982 
  -982   -982    -66    145 
   162   -982   -982   -982 
   104   -982   -982      4 
   126    -66    -66   -982 
    45    166   -982   -982 
  -982   -982    251   -982 
   145   -982    -66   -982 
  -982   -982    234   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 7.4e-007 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.666667  0.000000  0.333333 
 0.000000  0.333333  0.666667  0.000000 
 0.222222  0.555556  0.000000  0.222222 
 0.333333  0.222222  0.222222  0.222222 
 0.000000  0.333333  0.000000  0.666667 
 0.111111  0.555556  0.333333  0.000000 
 0.555556  0.444444  0.000000  0.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  0.444444  0.555556 
 0.000000  0.000000  0.000000  1.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.000000  0.111111  0.888889 
 1.000000  0.000000  0.000000  0.000000 
 0.666667  0.000000  0.000000  0.333333 
 0.777778  0.111111  0.111111  0.000000 
 0.444444  0.555556  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.000000  0.888889  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
C[CT][GC][CAT][ACGTC][TC][CG][AC]T[TG]TATA[AT]A[CA]GAG
--------------------------------------------------------------------------------




Time 23.77 secs.

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


********************************************************************************
MOTIF  4	width =   15   sites =   9   llr = 130   E-value = 2.3e-003
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  :::4::4:8::::18
pos.-specific     C  ::131::2::8:99:
probability       G  :921:94::92a::1
matrix            T  a171911821::1:1

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

Multilevel           TGTATGATAGCGCCA
consensus              GC  GCT G    
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Skud_Contig1362.1      +    248  5.26e-10 ACAGAGGAAG TGTATGGTAGCGCCA AGGAAAACGG
MIT_Spar_c130_3923           +    289  5.26e-10 AAAAAAATCG TGTATGGTAGCGCCA AGATAGCGAA
SGD_Scer_YDR047W             +    291  2.07e-09 AAAAAGATCG TGTATGATAGCGCCA AGATGGCGGA
MIT_Sbay_c896_21277          +    241  3.97e-09 ACGAGGAAGC TGCATGGTAGCGCCA GAAAAGGCAG
MIT_Spar_c19_8512            +     78  7.03e-08 TTGTTTTATG TGGCTGATTGGGCCA AAAAACAAGG
MIT_Sbay_c77_8808            -    909  8.89e-08 TTAAACATGA TGTCTGACATCGCCA TAACGACTAA
SGD_Scer_YGL040C             +     76  7.23e-07 TTTTTTTATT TGGCTGATTGGGCAA GAAAATCAAA
MIT_Smik_c273_7756           +    256  2.61e-06 CTACCAATTT TTTTCGGCAGCGCCT TTGAATGACT
WashU_Skud_Contig2052.17     +    462  5.54e-06 TTCTTGAATT TGTGTTTTAGCGTCG ATGAAGACTC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1362.1           5.3e-10  247_[+4]_499
MIT_Spar_c130_3923                5.3e-10  288_[+4]_697
SGD_Scer_YDR047W                  2.1e-09  290_[+4]_695
MIT_Sbay_c896_21277                 4e-09  240_[+4]_745
MIT_Spar_c19_8512                   7e-08  77_[+4]_908
MIT_Sbay_c77_8808                 8.9e-08  908_[-4]_77
SGD_Scer_YGL040C                  7.2e-07  75_[+4]_910
MIT_Smik_c273_7756                2.6e-06  255_[+4]_730
WashU_Skud_Contig2052.17          5.5e-06  461_[+4]_524
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=15 seqs=9
WashU_Skud_Contig1362.1  (  248) TGTATGGTAGCGCCA  1 
MIT_Spar_c130_3923       (  289) TGTATGGTAGCGCCA  1 
SGD_Scer_YDR047W         (  291) TGTATGATAGCGCCA  1 
MIT_Sbay_c896_21277      (  241) TGCATGGTAGCGCCA  1 
MIT_Spar_c19_8512        (   78) TGGCTGATTGGGCCA  1 
MIT_Sbay_c77_8808        (  909) TGTCTGACATCGCCA  1 
SGD_Scer_YGL040C         (   76) TGGCTGATTGGGCAA  1 
MIT_Smik_c273_7756       (  256) TTTTCGGCAGCGCCT  1 
WashU_Skud_Contig2052.17 (  462) TGTGTTTTAGCGTCG  1 
//

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

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 8635 bayes= 9.90455 E= 2.3e-003 
  -982   -982   -982    162 
  -982   -982    234   -154 
  -982    -66     34    104 
    45     92    -66   -154 
  -982    -66   -982    145 
  -982   -982    234   -154 
    45   -982    134   -154 
  -982     34   -982    126 
   126   -982   -982    -55 
  -982   -982    234   -154 
  -982    215     34   -982 
  -982   -982    251   -982 
  -982    234   -982   -154 
  -154    234   -982   -982 
   126   -982    -66   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 2.3e-003 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.888889  0.111111 
 0.000000  0.111111  0.222222  0.666667 
 0.444444  0.333333  0.111111  0.111111 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  0.888889  0.111111 
 0.444444  0.000000  0.444444  0.111111 
 0.000000  0.222222  0.000000  0.777778 
 0.777778  0.000000  0.000000  0.222222 
 0.000000  0.000000  0.888889  0.111111 
 0.000000  0.777778  0.222222  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.111111  0.888889  0.000000  0.000000 
 0.777778  0.000000  0.111111  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
TG[TG][AC]TG[AG][TC][AT]G[CG]GCCA
--------------------------------------------------------------------------------




Time 31.71 secs.

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


********************************************************************************
MOTIF  5	width =   20   sites =   9   llr = 145   E-value = 2.1e-001
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  7336939a283881:9:2:8
pos.-specific     C  32:::6:::2::::2:8:a2
probability       G  :264111:::722281:8::
matrix            T  :21:::::8::::7::2:::

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

Multilevel           AAGAACAATAGAATGACGCA
consensus            CCAG A  ACAGGGC TA C
sequence              G                  
                      T                  
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Smik_c273_7756           +     99  6.39e-12 CCAATAAATC AGGAACAATAGAATGACGCA CCGAGTTTGC
WashU_Skud_Contig2052.17     +     97  1.53e-10 GCCAGAAATC ATGAACAATAGGATGACGCA TAGACGTCAC
MIT_Spar_c19_8512            +     99  3.15e-10 GCCAAAAAAC AAGGACAATAGAATGACACA TAAAGTTTGC
SGD_Scer_YGL040C             +     98  2.76e-09 CAAGAAAATC AAAGACAATAGAGTGGCGCA TAGATGTTGC
MIT_Spar_c130_3923           -    817  3.44e-08 GATTTGTCGG CCGGAAAAAAAAAGCACGCA TCCGGCAAGG
SGD_Scer_YDR047W             -    807  3.44e-08 TATGTGTCGG CCGGAAAAAAAAAGCACGCA TCCGGCAAGC
MIT_Sbay_c77_8808            +    102  4.32e-08 ATGAACTAAC ATTAACAATAGAGTGATGCA TAGACGTCAC
MIT_Sbay_c896_21277          +    549  2.76e-07 ATATGCCCAG CAAAGGGATCGGATGACGCC CAACTAACAT
WashU_Skud_Contig1362.1      -     10  8.14e-07 CTACCAATCT AGAAAAAATCAAAAGATACC ATCAACACT 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c273_7756                6.4e-12  98_[+5]_882
WashU_Skud_Contig2052.17          1.5e-10  96_[+5]_884
MIT_Spar_c19_8512                 3.1e-10  98_[+5]_882
SGD_Scer_YGL040C                  2.8e-09  97_[+5]_883
MIT_Spar_c130_3923                3.4e-08  816_[-5]_164
SGD_Scer_YDR047W                  3.4e-08  806_[-5]_174
MIT_Sbay_c77_8808                 4.3e-08  101_[+5]_879
MIT_Sbay_c896_21277               2.8e-07  548_[+5]_432
WashU_Skud_Contig1362.1           8.1e-07  9_[-5]_732
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=9
MIT_Smik_c273_7756       (   99) AGGAACAATAGAATGACGCA  1 
WashU_Skud_Contig2052.17 (   97) ATGAACAATAGGATGACGCA  1 
MIT_Spar_c19_8512        (   99) AAGGACAATAGAATGACACA  1 
SGD_Scer_YGL040C         (   98) AAAGACAATAGAGTGGCGCA  1 
MIT_Spar_c130_3923       (  817) CCGGAAAAAAAAAGCACGCA  1 
SGD_Scer_YDR047W         (  807) CCGGAAAAAAAAAGCACGCA  1 
MIT_Sbay_c77_8808        (  102) ATTAACAATAGAGTGATGCA  1 
MIT_Sbay_c896_21277      (  549) CAAAGGGATCGGATGACGCC  1 
WashU_Skud_Contig1362.1  (   10) AGAAAAAATCAAAAGATACC  1 
//

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

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 8590 bayes= 9.89701 E= 2.1e-001 
   104     92   -982   -982 
     4     34     34    -55 
     4   -982    166   -154 
    78   -982    134   -982 
   145   -982    -66   -982 
     4    166    -66   -982 
   145   -982    -66   -982 
   162   -982   -982   -982 
   -55   -982   -982    126 
   126     34   -982   -982 
     4   -982    192   -982 
   126   -982     34   -982 
   126   -982     34   -982 
  -154   -982     34    104 
  -982     34    215   -982 
   145   -982    -66   -982 
  -982    215   -982    -55 
   -55   -982    215   -982 
  -982    251   -982   -982 
   126     34   -982   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.1e-001 
 0.666667  0.333333  0.000000  0.000000 
 0.333333  0.222222  0.222222  0.222222 
 0.333333  0.000000  0.555556  0.111111 
 0.555556  0.000000  0.444444  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.333333  0.555556  0.111111  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.222222  0.000000  0.000000  0.777778 
 0.777778  0.222222  0.000000  0.000000 
 0.333333  0.000000  0.666667  0.000000 
 0.777778  0.000000  0.222222  0.000000 
 0.777778  0.000000  0.222222  0.000000 
 0.111111  0.000000  0.222222  0.666667 
 0.000000  0.222222  0.777778  0.000000 
 0.888889  0.000000  0.111111  0.000000 
 0.000000  0.777778  0.000000  0.222222 
 0.222222  0.000000  0.777778  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.777778  0.222222  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
[AC][ACGTC][GA][AG]A[CA]AA[TA][AC][GA][AG][AG][TG][GC]A[CT][GA]C[AC]
--------------------------------------------------------------------------------




Time 39.58 secs.

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


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

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YGL040C                 1.84e-25  75_[+4(7.23e-07)]_7_[+5(2.76e-09)]_32_[-3(1.63e-09)]_9_[+1(4.85e-12)]_2_[+2(3.60e-13)]_780
MIT_Spar_c19_8512                1.53e-29  19_[+2(8.47e-05)]_38_[+4(7.03e-08)]_6_[+5(3.15e-10)]_32_[-3(6.18e-10)]_9_[+1(5.70e-14)]_2_[+2(3.60e-13)]_229_[-1(3.52e-05)]_530
MIT_Smik_c273_7756               2.73e-25  98_[+5(6.39e-12)]_59_[+1(5.70e-14)]_2_[+2(6.88e-11)]_3_[-5(1.42e-05)]_13_[+4(2.61e-06)]_600_[+3(1.32e-07)]_110
MIT_Sbay_c77_8808                2.58e-22  101_[+5(4.32e-08)]_33_[-3(1.63e-09)]_5_[+1(4.81e-13)]_1_[+2(4.15e-09)]_688_[-4(8.89e-08)]_77
WashU_Skud_Contig2052.17         7.43e-27  96_[+5(1.53e-10)]_33_[-3(1.10e-08)]_9_[+1(5.70e-14)]_2_[+2(3.60e-13)]_241_[+4(5.54e-06)]_44_[-5(8.79e-05)]_430_[+1(9.64e-05)]_10
SGD_Scer_YDR047W                 1.12e-21  19_[-5(5.14e-05)]_166_[-5(2.78e-05)]_27_[+3(7.00e-10)]_18_[+4(2.07e-09)]_76_[+2(5.89e-06)]_155_[+2(2.56e-09)]_39_[+1(4.68e-10)]_171_[-5(3.44e-08)]_99_[+1(4.63e-05)]_55
MIT_Spar_c130_3923               9.38e-21  92_[+4(5.51e-05)]_142_[+3(4.40e-09)]_19_[+4(5.26e-10)]_250_[+2(1.46e-08)]_38_[+1(4.99e-10)]_185_[-5(3.44e-08)]_82_[+2(5.53e-06)]_62
MIT_Sbay_c896_21277              1.53e-20  38_[-2(1.46e-08)]_114_[-5(6.18e-05)]_23_[+3(1.03e-10)]_5_[+4(3.97e-09)]_293_[+5(2.76e-07)]_121_[-4(7.12e-06)]_48_[+1(6.93e-05)]_123_[+1(5.96e-10)]_85
WashU_Skud_Contig1362.1          9.11e-19  9_[-5(8.14e-07)]_55_[-1(1.36e-05)]_106_[+3(8.03e-09)]_17_[+4(5.26e-10)]_1_[-2(2.12e-08)]_330_[+1(4.38e-09)]_99_[-1(7.81e-06)]_9
--------------------------------------------------------------------------------

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


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

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

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