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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= HEM2-HEM4.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_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  
********************************************************************************

********************************************************************************
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-HEM4.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=       10    maxsites=       10    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            8175    N=              10
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.324 C 0.176 G 0.176 T 0.324 
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 =  10   llr = 209   E-value = 6.2e-024
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :aa:5a5:::a:::44:416
pos.-specific     C  a:::5:5a:5:5a:169:::
probability       G  ::::::::55:::5:::694
matrix            T  :::a::::5::5:55:1:::

         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           CAATAAACGCACCGTCCGGA
consensus                C C TG T TAA A G
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Sbay_c77_8808            +    187  6.45e-12 TGCCGCAGGC CAATCACCGCACCGCCCGGA GATGCTCGTT
WashU_Skud_Contig2052.17     +    186  6.21e-11 TGCCTCAGGC CAATCACCGCACCGAACAGG GATTGCTCGT
MIT_Spar_c19_8512            +    187  6.21e-11 TGCCTCAGGC CAATCACCGCACCGAACAGG GATTGCTCGT
SGD_Scer_YGL040C             +    186  6.21e-11 TGCCTCAAGC CAATCACCGCACCGAACAGG GATTGCTCGT
WashU_Sbay_Contig635.57      -    400  2.02e-10 AGCCATCATT CAATAAACTGATCTTCCGGA TTACCATGCT
WashU_Skud_Contig1682.4      -    393  2.02e-10 AACCATCATT CAATAAACTGATCTTCCGGA TTACCATGCT
MIT_Smik_c492_20940          -    398  2.02e-10 AACCATCATT CAATAAACTGATCTTCCGGA TTACCATGCT
MIT_Spar_c261_21317          -    392  2.02e-10 AACCATCATT CAATAAACTGATCTTCCGGA TTACCATGCT
SGD_Scer_YOR278W             -    389  2.02e-10 AACCATCATT CAATAAACTGATCTTCCGGA TTACCATGCT
MIT_Smik_c273_7756           +    185  3.21e-09 TGCCTCAGGC CAATCACCGCACCGAATAAG GATTGCTCGT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Sbay_c77_8808                 6.4e-12  186_[+1]_794
WashU_Skud_Contig2052.17          6.2e-11  185_[+1]_795
MIT_Spar_c19_8512                 6.2e-11  186_[+1]_794
SGD_Scer_YGL040C                  6.2e-11  185_[+1]_795
WashU_Sbay_Contig635.57             2e-10  399_[-1]_216
WashU_Skud_Contig1682.4             2e-10  392_[-1]_223
MIT_Smik_c492_20940                 2e-10  397_[-1]_218
MIT_Spar_c261_21317                 2e-10  391_[-1]_224
SGD_Scer_YOR278W                    2e-10  388_[-1]_227
MIT_Smik_c273_7756                3.2e-09  184_[+1]_796
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=10
MIT_Sbay_c77_8808        (  187) CAATCACCGCACCGCCCGGA  1 
WashU_Skud_Contig2052.17 (  186) CAATCACCGCACCGAACAGG  1 
MIT_Spar_c19_8512        (  187) CAATCACCGCACCGAACAGG  1 
SGD_Scer_YGL040C         (  186) CAATCACCGCACCGAACAGG  1 
WashU_Sbay_Contig635.57  (  400) CAATAAACTGATCTTCCGGA  1 
WashU_Skud_Contig1682.4  (  393) CAATAAACTGATCTTCCGGA  1 
MIT_Smik_c492_20940      (  398) CAATAAACTGATCTTCCGGA  1 
MIT_Spar_c261_21317      (  392) CAATAAACTGATCTTCCGGA  1 
SGD_Scer_YOR278W         (  389) CAATAAACTGATCTTCCGGA  1 
MIT_Smik_c273_7756       (  185) CAATCACCGCACCGAATAAG  1 
//

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

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7985 bayes= 9.63934 E= 6.2e-024 
  -997    251   -997   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
  -997   -997   -997    162 
    62    151   -997   -997 
   162   -997   -997   -997 
    62    151   -997   -997 
  -997    251   -997   -997 
  -997   -997    151     62 
  -997    151    151   -997 
   162   -997   -997   -997 
  -997    151   -997     62 
  -997    251   -997   -997 
  -997   -997    151     62 
    30    -81   -997     62 
    30    177   -997   -997 
  -997    236   -997   -169 
    30   -997    177   -997 
  -169   -997    236   -997 
    89   -997    119   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 6.2e-024 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.500000  0.500000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  0.500000  0.500000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.500000  0.500000 
 0.400000  0.100000  0.000000  0.500000 
 0.400000  0.600000  0.000000  0.000000 
 0.000000  0.900000  0.000000  0.100000 
 0.400000  0.000000  0.600000  0.000000 
 0.100000  0.000000  0.900000  0.000000 
 0.600000  0.000000  0.400000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
CAAT[AC]A[AC]C[GT][CG]A[CT]C[GT][TA][CA]C[GA]G[AG]
--------------------------------------------------------------------------------




Time  6.87 secs.

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


********************************************************************************
MOTIF  2	width =   15   sites =  10   llr = 166   E-value = 1.6e-014
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  7:51a::5::::::5
pos.-specific     C  :::8::915:aa:a5
probability       G  395::41::a::1::
matrix            T  :1:1:6:45:::9::

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

Multilevel           AGACATCACGCCTCA
consensus            G G  G TT     C
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Sbay_Contig635.57      -    373  1.33e-09 ACCATGCTTA AGACATCACGCCTCC ATATGTCTAT
WashU_Skud_Contig1682.4      -    366  1.33e-09 ACCATGCTTA AGACATCACGCCTCC ATATGTCTAT
MIT_Smik_c492_20940          -    371  1.33e-09 ACCATGCTTA AGACATCACGCCTCC ATATGTCTAT
MIT_Spar_c261_21317          -    365  1.33e-09 ACCATGCTTA AGACATCACGCCTCC ATATGTCTAT
SGD_Scer_YOR278W             -    362  1.33e-09 ACCATGCTTA AGACATCACGCCTCC ATATGTCTAT
WashU_Skud_Contig2052.17     +    168  5.67e-09 TAAATTGGGC AGGCAGCTTGCCTCA GGCCAATCAC
MIT_Spar_c19_8512            +    169  7.74e-09 TAAATCAAGC GGGCAGCTTGCCTCA GGCCAATCAC
MIT_Sbay_c77_8808            +    169  4.53e-08 TTTATAAATC AGGCAGCCTGCCGCA GGCCAATCAC
SGD_Scer_YGL040C             +    168  7.07e-08 TAAATCAAGC GGGAAGCTTGCCTCA AGCCAATCAC
MIT_Smik_c273_7756           +    167  6.43e-07 TAAATCAAGA GTGTATGTTGCCTCA GGCCAATCAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           1.3e-09  372_[-2]_248
WashU_Skud_Contig1682.4           1.3e-09  365_[-2]_255
MIT_Smik_c492_20940               1.3e-09  370_[-2]_250
MIT_Spar_c261_21317               1.3e-09  364_[-2]_256
SGD_Scer_YOR278W                  1.3e-09  361_[-2]_259
WashU_Skud_Contig2052.17          5.7e-09  167_[+2]_818
MIT_Spar_c19_8512                 7.7e-09  168_[+2]_817
MIT_Sbay_c77_8808                 4.5e-08  168_[+2]_817
SGD_Scer_YGL040C                  7.1e-08  167_[+2]_818
MIT_Smik_c273_7756                6.4e-07  166_[+2]_819
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=15 seqs=10
WashU_Sbay_Contig635.57  (  373) AGACATCACGCCTCC  1 
WashU_Skud_Contig1682.4  (  366) AGACATCACGCCTCC  1 
MIT_Smik_c492_20940      (  371) AGACATCACGCCTCC  1 
MIT_Spar_c261_21317      (  365) AGACATCACGCCTCC  1 
SGD_Scer_YOR278W         (  362) AGACATCACGCCTCC  1 
WashU_Skud_Contig2052.17 (  168) AGGCAGCTTGCCTCA  1 
MIT_Spar_c19_8512        (  169) GGGCAGCTTGCCTCA  1 
MIT_Sbay_c77_8808        (  169) AGGCAGCCTGCCGCA  1 
SGD_Scer_YGL040C         (  168) GGGAAGCTTGCCTCA  1 
MIT_Smik_c273_7756       (  167) GTGTATGTTGCCTCA  1 
//

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

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 8035 bayes= 9.64836 E= 1.6e-014 
   111   -997     77   -997 
  -997   -997    236   -169 
    62   -997    151   -997 
  -169    219   -997   -169 
   162   -997   -997   -997 
  -997   -997    119     89 
  -997    236    -81   -997 
    62    -81   -997     30 
  -997    151   -997     62 
  -997   -997    251   -997 
  -997    251   -997   -997 
  -997    251   -997   -997 
  -997   -997    -81    147 
  -997    251   -997   -997 
    62    151   -997   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 1.6e-014 
 0.700000  0.000000  0.300000  0.000000 
 0.000000  0.000000  0.900000  0.100000 
 0.500000  0.000000  0.500000  0.000000 
 0.100000  0.800000  0.000000  0.100000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.400000  0.600000 
 0.000000  0.900000  0.100000  0.000000 
 0.500000  0.100000  0.000000  0.400000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.100000  0.900000 
 0.000000  1.000000  0.000000  0.000000 
 0.500000  0.500000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
[AG]G[AG]CA[TG]C[AT][CT]GCCTC[AC]
--------------------------------------------------------------------------------




Time 13.73 secs.

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


********************************************************************************
MOTIF  3	width =   20   sites =  10   llr = 189   E-value = 4.3e-016
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :a1:1a:71::7:911596:
pos.-specific     C  1:1:::5:7a:::::6:::7
probability       G  :::a4::1:::3a191514:
matrix            T  9:8:5:522:a::::2:::3

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

Multilevel           TATGTACACCTAGAGCAAAC
consensus                G TTT  G   TG GT
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig1682.4      +    225  1.88e-12 GAAGTAGAGA TATGTACACCTAGAGCGAAC CAATGATAAT
MIT_Smik_c492_20940          +    228  1.88e-12 GAAGTGAAGA TATGTACACCTAGAGCGAAC CAATAATAAT
MIT_Spar_c261_21317          +    223  1.88e-12 ACAAAATGAA TATGTACACCTAGAGCGAAC CAATGATAAT
SGD_Scer_YOR278W             +    219  1.88e-12 GAAGTGAAGA TATGTACACCTAGAGCGAAC CAATGATAAT
WashU_Sbay_Contig635.57      +    231  4.24e-11 GTAAAAAAAA CATGTACACCTAGAGCGAAC CAGTGATAAT
MIT_Spar_c19_8512            +     21  3.25e-09 ATATTCTAAA TATGGATTCCTAGGGCAGGC AATAATATGG
WashU_Skud_Contig2052.17     +     21  7.96e-09 TGTTTTCTGA TATGGATGCCTGGAGAAAAT ATTAATATGT
MIT_Smik_c273_7756           +     21  1.42e-08 GTTTTCTTAA TACGGATATCTAGAGTAAGT CACAATTTAA
SGD_Scer_YGL040C             +     21  2.94e-08 ATTTTCTAGG TATGAATTACTGGAGTAAGC AATAATATGA
MIT_Sbay_c77_8808            +     22  8.75e-08 GTTTTTCTGG TAAGGATATCTGGAAGAAGT AACAATACGT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1682.4           1.9e-12  224_[+3]_391
MIT_Smik_c492_20940               1.9e-12  227_[+3]_388
MIT_Spar_c261_21317               1.9e-12  222_[+3]_393
SGD_Scer_YOR278W                  1.9e-12  218_[+3]_397
WashU_Sbay_Contig635.57           4.2e-11  230_[+3]_385
MIT_Spar_c19_8512                 3.2e-09  20_[+3]_960
WashU_Skud_Contig2052.17            8e-09  20_[+3]_960
MIT_Smik_c273_7756                1.4e-08  20_[+3]_960
SGD_Scer_YGL040C                  2.9e-08  20_[+3]_960
MIT_Sbay_c77_8808                 8.8e-08  21_[+3]_959
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=10
WashU_Skud_Contig1682.4  (  225) TATGTACACCTAGAGCGAAC  1 
MIT_Smik_c492_20940      (  228) TATGTACACCTAGAGCGAAC  1 
MIT_Spar_c261_21317      (  223) TATGTACACCTAGAGCGAAC  1 
SGD_Scer_YOR278W         (  219) TATGTACACCTAGAGCGAAC  1 
WashU_Sbay_Contig635.57  (  231) CATGTACACCTAGAGCGAAC  1 
MIT_Spar_c19_8512        (   21) TATGGATTCCTAGGGCAGGC  1 
WashU_Skud_Contig2052.17 (   21) TATGGATGCCTGGAGAAAAT  1 
MIT_Smik_c273_7756       (   21) TACGGATATCTAGAGTAAGT  1 
SGD_Scer_YGL040C         (   21) TATGAATTACTGGAGTAAGC  1 
MIT_Sbay_c77_8808        (   22) TAAGGATATCTGGAAGAAGT  1 
//

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

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7985 bayes= 9.63934 E= 4.3e-016 
  -997    -81   -997    147 
   162   -997   -997   -997 
  -169    -81   -997    130 
  -997   -997    251   -997 
  -169   -997    119     62 
   162   -997   -997   -997 
  -997    151   -997     62 
   111   -997    -81    -70 
  -169    199   -997    -70 
  -997    251   -997   -997 
  -997   -997   -997    162 
   111   -997     77   -997 
  -997   -997    251   -997 
   147   -997    -81   -997 
  -169   -997    236   -997 
  -169    177    -81    -70 
    62   -997    151   -997 
   147   -997    -81   -997 
    89   -997    119   -997 
  -997    199   -997    -11 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 4.3e-016 
 0.000000  0.100000  0.000000  0.900000 
 1.000000  0.000000  0.000000  0.000000 
 0.100000  0.100000  0.000000  0.800000 
 0.000000  0.000000  1.000000  0.000000 
 0.100000  0.000000  0.400000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.700000  0.000000  0.100000  0.200000 
 0.100000  0.700000  0.000000  0.200000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.700000  0.000000  0.300000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.900000  0.000000  0.100000  0.000000 
 0.100000  0.000000  0.900000  0.000000 
 0.100000  0.600000  0.100000  0.200000 
 0.500000  0.000000  0.500000  0.000000 
 0.900000  0.000000  0.100000  0.000000 
 0.600000  0.000000  0.400000  0.000000 
 0.000000  0.700000  0.000000  0.300000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
TATG[TG]A[CT][AT][CT]CT[AG]GAG[CT][AG]A[AG][CT]
--------------------------------------------------------------------------------




Time 20.40 secs.

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


********************************************************************************
MOTIF  4	width =   20   sites =  10   llr = 176   E-value = 2.5e-011
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  ::6:11::72::7::1:::2
pos.-specific     C  a:19::882:68::::29:6
probability       G  ::::1:11:62:1:126192
matrix            T  :a31891112222a972:1:

         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           CTACTTCCAGCCATTTGCGC
consensus              T     CAGTT  GC  A
sequence                      TT     T  G
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Sbay_Contig635.57      +    338  1.95e-13 AGAAATTGGT CTACTTCCAGCCATTTGCGC TTGACATAGA
WashU_Skud_Contig1682.4      +    331  1.95e-13 AGAGATTGGT CTACTTCCAGCCATTTGCGC TTTACATAGA
MIT_Smik_c492_20940          +    336  1.95e-13 AGAAATTTGT CTACTTCCAGCCATTTGCGC TTTATATAGA
MIT_Spar_c261_21317          +    330  1.95e-13 AAAAATTGGT CTACTTCCAGCCATTTGCGC TTTATATAGA
SGD_Scer_YOR278W             +    327  1.95e-13 AAAAATTGGT CTACTTCCAGCCATTTGCGC TTTATATAGA
SGD_Scer_YGL040C             +    444  9.32e-08 ACGTGTACGC CTTCTTCCCTTCTTTGCCTC TTGTGCCACT
MIT_Smik_c273_7756           +    243  2.84e-07 TTTTTTTCAT CTTCTACCAATTTTTTTCGG CAGCGCCTTT
WashU_Skud_Contig2052.17     -    956  5.15e-07 TGTAGTTTTC CTTCGTTCAGCCATGACGGA AACTACATAA
MIT_Spar_c19_8512            -    872  8.90e-07 TCATTAACCT CTCCATCTTTGTATTGGCGG TACGACATAT
MIT_Sbay_c77_8808            +    255  1.31e-06 TTGCCTTTTT CTATTTGGCAGCGTTTTCGA AAAATTTTGA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Sbay_Contig635.57           1.9e-13  337_[+4]_278
WashU_Skud_Contig1682.4           1.9e-13  330_[+4]_285
MIT_Smik_c492_20940               1.9e-13  335_[+4]_280
MIT_Spar_c261_21317               1.9e-13  329_[+4]_286
SGD_Scer_YOR278W                  1.9e-13  326_[+4]_289
SGD_Scer_YGL040C                  9.3e-08  443_[+4]_537
MIT_Smik_c273_7756                2.8e-07  242_[+4]_738
WashU_Skud_Contig2052.17          5.1e-07  955_[-4]_25
MIT_Spar_c19_8512                 8.9e-07  871_[-4]_109
MIT_Sbay_c77_8808                 1.3e-06  254_[+4]_726
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=10
WashU_Sbay_Contig635.57  (  338) CTACTTCCAGCCATTTGCGC  1 
WashU_Skud_Contig1682.4  (  331) CTACTTCCAGCCATTTGCGC  1 
MIT_Smik_c492_20940      (  336) CTACTTCCAGCCATTTGCGC  1 
MIT_Spar_c261_21317      (  330) CTACTTCCAGCCATTTGCGC  1 
SGD_Scer_YOR278W         (  327) CTACTTCCAGCCATTTGCGC  1 
SGD_Scer_YGL040C         (  444) CTTCTTCCCTTCTTTGCCTC  1 
MIT_Smik_c273_7756       (  243) CTTCTACCAATTTTTTTCGG  1 
WashU_Skud_Contig2052.17 (  956) CTTCGTTCAGCCATGACGGA  1 
MIT_Spar_c19_8512        (  872) CTCCATCTTTGTATTGGCGG  1 
MIT_Sbay_c77_8808        (  255) CTATTTGGCAGCGTTTTCGA  1 
//

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

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7985 bayes= 9.63934 E= 2.5e-011 
  -997    251   -997   -997 
  -997   -997   -997    162 
    89    -81   -997    -11 
  -997    236   -997   -169 
  -169   -997    -81    130 
  -169   -997   -997    147 
  -997    219    -81   -169 
  -997    219    -81   -169 
   111     19   -997   -169 
   -70   -997    177    -70 
  -997    177     19    -70 
  -997    219   -997    -70 
   111   -997    -81    -70 
  -997   -997   -997    162 
  -997   -997    -81    147 
  -169   -997     19    111 
  -997     19    177    -70 
  -997    236    -81   -997 
  -997   -997    236   -169 
   -70    177     19   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.5e-011 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.600000  0.100000  0.000000  0.300000 
 0.000000  0.900000  0.000000  0.100000 
 0.100000  0.000000  0.100000  0.800000 
 0.100000  0.000000  0.000000  0.900000 
 0.000000  0.800000  0.100000  0.100000 
 0.000000  0.800000  0.100000  0.100000 
 0.700000  0.200000  0.000000  0.100000 
 0.200000  0.000000  0.600000  0.200000 
 0.000000  0.600000  0.200000  0.200000 
 0.000000  0.800000  0.000000  0.200000 
 0.700000  0.000000  0.100000  0.200000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.100000  0.900000 
 0.100000  0.000000  0.200000  0.700000 
 0.000000  0.200000  0.600000  0.200000 
 0.000000  0.900000  0.100000  0.000000 
 0.000000  0.000000  0.900000  0.100000 
 0.200000  0.600000  0.200000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
CT[AT]CTTCC[AC][GAT][CGT][CT][AT]TT[TG][GCT]CG[CAG]
--------------------------------------------------------------------------------




Time 26.90 secs.

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


********************************************************************************
MOTIF  5	width =   20   sites =  10   llr = 171   E-value = 2.2e-009
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  8a327aaa21:71:9a1987
pos.-specific     C  1::::::::8::::1:6:12
probability       G  ::18::::81:269::1111
matrix            T  1:6:3:::::a131::2:::

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

Multilevel           AATGAAAAGCTAGGAACAAA
consensus              AAT   A  GT   T  C
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Smik_c492_20940          +    306  4.19e-12 AGATTTCAAT AATGAAAAGCTAGGAACAAA AGAAATTTGT
SGD_Scer_YOR278W             +    297  4.19e-12 AGATTTCAAT AATGAAAAGCTAGGAACAAA AAAAATTGGT
WashU_Sbay_Contig635.57      +    309  1.29e-11 AGATTTCATT AAAGAAAAGCTAGGAACAAA GAAATTGGTC
MIT_Spar_c261_21317          +    301  4.20e-11 AGATTTCAAT AATGAAAAGCTAGGAACAGA AAAATTGGTC
WashU_Skud_Contig1682.4      +    301  6.30e-11 AGATTTCAAT AATGAAAAGCTAGGAATAAA AGAGATTGGT
MIT_Sbay_c77_8808            +    327  4.84e-08 TTAGGGCACG CAGGTAAAGATATGAACAAA TCATATTGAT
MIT_Spar_c19_8512            +    700  7.12e-08 TTCTTGATTG AAAATAAAGCTGTGAAGAAC TAAATAATAA
WashU_Skud_Contig2052.17     -    224  8.93e-08 TGATGCGGAA AATGAAAAACTTTGAACGCA ACGGGTAAAC
SGD_Scer_YGL040C             +    692  5.38e-07 TGTGCGAATT AAAGTAAAGCTAATCAAAAC TAAACAATAA
MIT_Smik_c273_7756           -    444  7.12e-07 TAACGATAAC TATAAAAAAGTGGGAATAAG ATATACACAT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Smik_c492_20940               4.2e-12  305_[+5]_310
SGD_Scer_YOR278W                  4.2e-12  296_[+5]_319
WashU_Sbay_Contig635.57           1.3e-11  308_[+5]_307
MIT_Spar_c261_21317               4.2e-11  300_[+5]_315
WashU_Skud_Contig1682.4           6.3e-11  300_[+5]_315
MIT_Sbay_c77_8808                 4.8e-08  326_[+5]_654
MIT_Spar_c19_8512                 7.1e-08  699_[+5]_281
WashU_Skud_Contig2052.17          8.9e-08  223_[-5]_757
SGD_Scer_YGL040C                  5.4e-07  691_[+5]_289
MIT_Smik_c273_7756                7.1e-07  443_[-5]_537
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=10
MIT_Smik_c492_20940      (  306) AATGAAAAGCTAGGAACAAA  1 
SGD_Scer_YOR278W         (  297) AATGAAAAGCTAGGAACAAA  1 
WashU_Sbay_Contig635.57  (  309) AAAGAAAAGCTAGGAACAAA  1 
MIT_Spar_c261_21317      (  301) AATGAAAAGCTAGGAACAGA  1 
WashU_Skud_Contig1682.4  (  301) AATGAAAAGCTAGGAATAAA  1 
MIT_Sbay_c77_8808        (  327) CAGGTAAAGATATGAACAAA  1 
MIT_Spar_c19_8512        (  700) AAAATAAAGCTGTGAAGAAC  1 
WashU_Skud_Contig2052.17 (  224) AATGAAAAACTTTGAACGCA  1 
SGD_Scer_YGL040C         (  692) AAAGTAAAGCTAATCAAAAC  1 
MIT_Smik_c273_7756       (  444) TATAAAAAAGTGGGAATAAG  1 
//

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

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7985 bayes= 9.63934 E= 2.2e-009 
   130    -81   -997   -169 
   162   -997   -997   -997 
   -11   -997    -81     89 
   -70   -997    219   -997 
   111   -997   -997    -11 
   162   -997   -997   -997 
   162   -997   -997   -997 
   162   -997   -997   -997 
   -70   -997    219   -997 
  -169    219    -81   -997 
  -997   -997   -997    162 
   111   -997     19   -169 
  -169   -997    177    -11 
  -997   -997    236   -169 
   147    -81   -997   -997 
   162   -997   -997   -997 
  -169    177    -81    -70 
   147   -997    -81   -997 
   130    -81    -81   -997 
   111     19    -81   -997 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 2.2e-009 
 0.800000  0.100000  0.000000  0.100000 
 1.000000  0.000000  0.000000  0.000000 
 0.300000  0.000000  0.100000  0.600000 
 0.200000  0.000000  0.800000  0.000000 
 0.700000  0.000000  0.000000  0.300000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.200000  0.000000  0.800000  0.000000 
 0.100000  0.800000  0.100000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.700000  0.000000  0.200000  0.100000 
 0.100000  0.000000  0.600000  0.300000 
 0.000000  0.000000  0.900000  0.100000 
 0.900000  0.100000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.100000  0.600000  0.100000  0.200000 
 0.900000  0.000000  0.100000  0.000000 
 0.800000  0.100000  0.100000  0.000000 
 0.700000  0.200000  0.100000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
AA[TA][GA][AT]AAA[GA]CT[AG][GT]GAA[CT]AA[AC]
--------------------------------------------------------------------------------




Time 33.38 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                 5.35e-17  20_[+3(2.94e-08)]_127_[+2(7.07e-08)]_3_[+1(6.21e-11)]_36_[-5(4.31e-05)]_84_[-4(9.17e-05)]_78_[+4(9.32e-08)]_228_[+5(5.38e-07)]_41_[-2(3.82e-05)]_74_[-3(7.54e-05)]_139
MIT_Spar_c19_8512                1.12e-18  20_[+3(3.25e-09)]_128_[+2(7.74e-09)]_3_[+1(6.21e-11)]_37_[-5(8.15e-05)]_436_[+5(7.12e-08)]_152_[-4(8.90e-07)]_109
MIT_Smik_c273_7756               2.75e-14  20_[+3(1.42e-08)]_126_[+2(6.43e-07)]_3_[+1(3.21e-09)]_38_[+4(2.84e-07)]_181_[-5(7.12e-07)]_537
MIT_Sbay_c77_8808                1.49e-17  21_[+3(8.75e-08)]_127_[+2(4.53e-08)]_3_[+1(6.45e-12)]_48_[+4(1.31e-06)]_52_[+5(4.84e-08)]_183_[+2(7.84e-05)]_348_[+4(1.00e-05)]_88
WashU_Skud_Contig2052.17         1.43e-18  20_[+3(7.96e-09)]_127_[+2(5.67e-09)]_3_[+1(6.21e-11)]_18_[-5(8.93e-08)]_712_[-4(5.15e-07)]_25
SGD_Scer_YOR278W                 3.31e-33  218_[+3(1.88e-12)]_58_[+5(4.19e-12)]_10_[+4(1.95e-13)]_15_[-2(1.33e-09)]_12_[-1(2.02e-10)]_181_[-5(9.56e-06)]_26
MIT_Spar_c261_21317              2.99e-32  222_[+3(1.88e-12)]_23_[+5(1.02e-05)]_15_[+5(4.20e-11)]_9_[+4(1.95e-13)]_15_[-2(1.33e-09)]_12_[-1(2.02e-10)]_224
MIT_Smik_c492_20940              3.31e-33  227_[+3(1.88e-12)]_23_[+5(1.02e-05)]_15_[+5(4.19e-12)]_10_[+4(1.95e-13)]_15_[-2(1.33e-09)]_12_[-1(2.02e-10)]_218
WashU_Skud_Contig1682.4          4.41e-32  224_[+3(1.88e-12)]_56_[+5(6.30e-11)]_10_[+4(1.95e-13)]_15_[-2(1.33e-09)]_12_[-1(2.02e-10)]_223
WashU_Sbay_Contig635.57          1.91e-31  230_[+3(4.24e-11)]_58_[+5(1.29e-11)]_9_[+4(1.95e-13)]_15_[-2(1.33e-09)]_12_[-1(2.02e-10)]_216
--------------------------------------------------------------------------------

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


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

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

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