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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= HEM3-HEM12.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
SGD_Scer_YDL205C         1.0000    860  MIT_Spar_c429_3020       1.0000    860  
MIT_Smik_c193_2483       1.0000    860  MIT_Sbay_c841_3215       1.0000    860  
WashU_Skud_Contig1850.5  1.0000    860  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 HEM3-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=            8061    N=               9
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.295 C 0.205 G 0.205 T 0.295 
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 = 189   E-value = 1.1e-018
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :784a4a4:::::4a::7::
pos.-specific     C  4321:6::aaa4:::9a3::
probability       G  1::::::6::::a::::::7
matrix            T  4::4:::::::6:6:1::a3

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

Multilevel           CAAAACAGCCCTGTACCATG
consensus            TCCT A A   C A   C T
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c429_3020           +    111  1.67e-11 ATTCAAAATG TAAAACAGCCCTGTACCATG CAAACACGAG
SGD_Scer_YDL205C             +    111  1.67e-11 ATTCAAAATC TAATACAGCCCTGTACCATG CAAACACGAG
WashU_Skud_Contig1850.5      +    111  5.77e-11 TTTCAAAAAG CAATACAGCCCTGTACCATT CAAACACGAA
MIT_Sbay_c841_3215           +    112  5.77e-11 ATTCAAAACG CAATACAGCCCTGTACCATT CAAATACGAA
MIT_Smik_c193_2483           +    113  1.63e-10 ATTCAAAAAG TAATACAGCCCTGTACCATT CAAACACGAG
MIT_Sbay_c896_21277          +    206  2.60e-10 TTCCATGGCG TCAAAAAACCCCGAACCCTG TATAAACGAG
MIT_Spar_c130_3923           +    235  4.70e-10 TCTCTCCTGC CACCAAAACCCCGAACCCTG TCCCGTATAT
SGD_Scer_YDR047W             +    238  7.68e-10 CTCTCCTGCC GCCAAAAACCCCGAACCCTG TCCTGTATAT
WashU_Skud_Contig1362.1      +    201  9.83e-10 TTTCCTGCTG CCAAAAAACCCCGAATCATG TAGAAGCGAG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c429_3020                1.7e-11  110_[+1]_730
SGD_Scer_YDL205C                  1.7e-11  110_[+1]_730
WashU_Skud_Contig1850.5           5.8e-11  110_[+1]_730
MIT_Sbay_c841_3215                5.8e-11  111_[+1]_729
MIT_Smik_c193_2483                1.6e-10  112_[+1]_728
MIT_Sbay_c896_21277               2.6e-10  205_[+1]_775
MIT_Spar_c130_3923                4.7e-10  234_[+1]_746
SGD_Scer_YDR047W                  7.7e-10  237_[+1]_743
WashU_Skud_Contig1362.1           9.8e-10  200_[+1]_541
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=9
MIT_Spar_c429_3020       (  111) TAAAACAGCCCTGTACCATG  1 
SGD_Scer_YDL205C         (  111) TAATACAGCCCTGTACCATG  1 
WashU_Skud_Contig1850.5  (  111) CAATACAGCCCTGTACCATT  1 
MIT_Sbay_c841_3215       (  112) CAATACAGCCCTGTACCATT  1 
MIT_Smik_c193_2483       (  113) TAATACAGCCCTGTACCATT  1 
MIT_Sbay_c896_21277      (  206) TCAAAAAACCCCGAACCCTG  1 
MIT_Spar_c130_3923       (  235) CACCAAAACCCCGAACCCTG  1 
SGD_Scer_YDR047W         (  238) GCCAAAAACCCCGAACCCTG  1 
WashU_Skud_Contig1362.1  (  201) CCAAAAAACCCCGAATCATG  1 
//

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

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7890 bayes= 9.77424 E= 1.1e-018 
  -982    134    -66     45 
   104     92   -982   -982 
   126     34   -982   -982 
    45    -66   -982     45 
   162   -982   -982   -982 
    45    166   -982   -982 
   162   -982   -982   -982 
    45   -982    166   -982 
  -982    251   -982   -982 
  -982    251   -982   -982 
  -982    251   -982   -982 
  -982    134   -982     78 
  -982   -982    251   -982 
    45   -982   -982     78 
   162   -982   -982   -982 
  -982    234   -982   -154 
  -982    251   -982   -982 
   104     92   -982   -982 
  -982   -982   -982    162 
  -982   -982    192      4 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.1e-018 
 0.000000  0.444444  0.111111  0.444444 
 0.666667  0.333333  0.000000  0.000000 
 0.777778  0.222222  0.000000  0.000000 
 0.444444  0.111111  0.000000  0.444444 
 1.000000  0.000000  0.000000  0.000000 
 0.444444  0.555556  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.444444  0.000000  0.555556 
 0.000000  0.000000  1.000000  0.000000 
 0.444444  0.000000  0.000000  0.555556 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  1.000000  0.000000  0.000000 
 0.666667  0.333333  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.666667  0.333333 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
[CT][AC][AC][AT]A[CA]A[GA]CCC[TC]G[TA]ACC[AC]T[GT]
--------------------------------------------------------------------------------




Time  6.92 secs.

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


********************************************************************************
MOTIF  2	width =   20   sites =   9   llr = 187   E-value = 6.5e-018
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  ::::1:11::4::a:3:a::
pos.-specific     C  68441:6:a::7a:::4:46
probability       G  ::::8a:9::61::676:63
matrix            T  4266::3::a:2::4::::1

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

Multilevel           CCTTGGCGCTGCCAGGGAGC
consensus            TTCC  T   AT  TAC CG
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
SGD_Scer_YDL205C             +    489  3.06e-13 ACATCTTTAC CCCCGGTGCTGCCAGGGAGC AAAATAATTA
MIT_Spar_c429_3020           +    493  9.57e-12 GACATCTTAC CCCCGGTGCTGTCAGGGAGC AAAAAAATGA
MIT_Sbay_c841_3215           +    503  2.31e-11 CCCTCCCCCT TCTCCGCGCTGCCAGGGACC AGGCAAGGGC
MIT_Sbay_c896_21277          -    239  1.64e-10 TATCTGCCTT TTCTGGCGCTACCATGCAGC TTCCTCGTTT
MIT_Spar_c130_3923           -    287  2.77e-10 TTATTCGCTA TCTTGGCGCTACCATACACG ATTTTTTTTC
WashU_Skud_Contig1850.5      +    494  5.55e-10 ACATCTTCAC CTTCGGAGCTGGCAGGGAGC AAGGGACTCT
WashU_Skud_Contig1362.1      -    246  6.00e-10 TGCCCGTTTT CCTTGGCGCTACCATACACT TCCTCTGTTT
SGD_Scer_YDR047W             -    289  1.18e-09 TTATCCGCCA TCTTGGCGCTATCATACACG ATCTTTTTCA
MIT_Smik_c193_2483           +    493  1.25e-09 TTCATCTTAC CCCTAGTACTGCCAGGGAGG AACTAAACCT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDL205C                  3.1e-13  488_[+2]_352
MIT_Spar_c429_3020                9.6e-12  492_[+2]_348
MIT_Sbay_c841_3215                2.3e-11  502_[+2]_338
MIT_Sbay_c896_21277               1.6e-10  238_[-2]_742
MIT_Spar_c130_3923                2.8e-10  286_[-2]_694
WashU_Skud_Contig1850.5           5.6e-10  493_[+2]_347
WashU_Skud_Contig1362.1             6e-10  245_[-2]_496
SGD_Scer_YDR047W                  1.2e-09  288_[-2]_692
MIT_Smik_c193_2483                1.3e-09  492_[+2]_348
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=9
SGD_Scer_YDL205C         (  489) CCCCGGTGCTGCCAGGGAGC  1 
MIT_Spar_c429_3020       (  493) CCCCGGTGCTGTCAGGGAGC  1 
MIT_Sbay_c841_3215       (  503) TCTCCGCGCTGCCAGGGACC  1 
MIT_Sbay_c896_21277      (  239) TTCTGGCGCTACCATGCAGC  1 
MIT_Spar_c130_3923       (  287) TCTTGGCGCTACCATACACG  1 
WashU_Skud_Contig1850.5  (  494) CTTCGGAGCTGGCAGGGAGC  1 
WashU_Skud_Contig1362.1  (  246) CCTTGGCGCTACCATACACT  1 
SGD_Scer_YDR047W         (  289) TCTTGGCGCTATCATACACG  1 
MIT_Smik_c193_2483       (  493) CCCTAGTACTGCCAGGGAGG  1 
//

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

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7890 bayes= 9.77424 E= 6.5e-018 
  -982    166   -982     45 
  -982    215   -982    -55 
  -982    134   -982     78 
  -982    134   -982     78 
  -154    -66    215   -982 
  -982   -982    251   -982 
  -154    166   -982      4 
  -154   -982    234   -982 
  -982    251   -982   -982 
  -982   -982   -982    162 
    45   -982    166   -982 
  -982    192    -66    -55 
  -982    251   -982   -982 
   162   -982   -982   -982 
  -982   -982    166     45 
     4   -982    192   -982 
  -982    134    166   -982 
   162   -982   -982   -982 
  -982    134    166   -982 
  -982    166     92   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.5e-018 
 0.000000  0.555556  0.000000  0.444444 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.444444  0.000000  0.555556 
 0.000000  0.444444  0.000000  0.555556 
 0.111111  0.111111  0.777778  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.111111  0.555556  0.000000  0.333333 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.444444  0.000000  0.555556  0.000000 
 0.000000  0.666667  0.111111  0.222222 
 0.000000  1.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.555556  0.444444 
 0.333333  0.000000  0.666667  0.000000 
 0.000000  0.444444  0.555556  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.444444  0.555556  0.000000 
 0.000000  0.555556  0.333333  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
[CT][CT][TC][TC]GG[CT]GCT[GA][CT]CA[GT][GA][GC]A[GC][CG]
--------------------------------------------------------------------------------




Time 13.49 secs.

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


********************************************************************************
MOTIF  3	width =   20   sites =   9   llr = 183   E-value = 1.9e-017
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :1::6:1::162::1:a:71
pos.-specific     C  :2::3a:1:22::a29::::
probability       G  a6:a1:9::::87:6::::8
matrix            T  :1a::::9a72:3:11:a31

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

Multilevel           GGTGACGTTTAGGCGCATAG
consensus             C  C    CCAT C   T 
sequence                       T         
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Skud_Contig1850.5      +    681  3.00e-13 AAAGTTGGAA GGTGACGTTTAGGCGCATAG GCAATCTCCC
MIT_Spar_c429_3020           +    674  3.00e-13 GAGGTTAGAG GGTGACGTTTAGGCGCATAG GCAACCTCCC
SGD_Scer_YDL205C             +    673  3.00e-13 AAGGTTAGAC GGTGACGTTTAGGCGCATAG GCAATCTCCC
MIT_Sbay_c841_3215           +    700  3.16e-11 AACATTAGAG GGTGACGTTTTAGCGCATAG GCAATCTCCC
MIT_Smik_c193_2483           +    674  1.45e-10 AAGGTCAGAG GATGACGTTTAAGCGCATAG GCAATCTCCC
MIT_Spar_c130_3923           +    713  2.43e-10 ACTCTAAAAT GCTGCCGTTCCGTCCCATTG AGTTTTATTT
SGD_Scer_YDR047W             +    713  2.43e-10 GTTAAAAAAT GCTGCCGTTCCGTCCCATTG AGTTTTATTT
WashU_Skud_Contig1362.1      +    703  2.69e-08 TCGATCGAAC GTTGCCGTTTAGTCTTATTT TCCTTTCCGT
MIT_Sbay_c896_21277          -    969  4.38e-08 GGGGGCTAGT GGTGGCACTATGGCACATAA AAGCCGTGCA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1850.5             3e-13  680_[+3]_160
MIT_Spar_c429_3020                  3e-13  673_[+3]_167
SGD_Scer_YDL205C                    3e-13  672_[+3]_168
MIT_Sbay_c841_3215                3.2e-11  699_[+3]_141
MIT_Smik_c193_2483                1.5e-10  673_[+3]_167
MIT_Spar_c130_3923                2.4e-10  712_[+3]_268
SGD_Scer_YDR047W                  2.4e-10  712_[+3]_268
WashU_Skud_Contig1362.1           2.7e-08  702_[+3]_39
MIT_Sbay_c896_21277               4.4e-08  968_[-3]_12
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=20 seqs=9
WashU_Skud_Contig1850.5  (  681) GGTGACGTTTAGGCGCATAG  1 
MIT_Spar_c429_3020       (  674) GGTGACGTTTAGGCGCATAG  1 
SGD_Scer_YDL205C         (  673) GGTGACGTTTAGGCGCATAG  1 
MIT_Sbay_c841_3215       (  700) GGTGACGTTTTAGCGCATAG  1 
MIT_Smik_c193_2483       (  674) GATGACGTTTAAGCGCATAG  1 
MIT_Spar_c130_3923       (  713) GCTGCCGTTCCGTCCCATTG  1 
SGD_Scer_YDR047W         (  713) GCTGCCGTTCCGTCCCATTG  1 
WashU_Skud_Contig1362.1  (  703) GTTGCCGTTTAGTCTTATTT  1 
MIT_Sbay_c896_21277      (  969) GGTGGCACTATGGCACATAA  1 
//

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

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7890 bayes= 9.77424 E= 1.9e-017 
  -982   -982    251   -982 
  -154     34    166   -154 
  -982   -982   -982    162 
  -982   -982    251   -982 
    78     92    -66   -982 
  -982    251   -982   -982 
  -154   -982    234   -982 
  -982    -66   -982    145 
  -982   -982   -982    162 
  -154     34   -982    104 
    78     34   -982    -55 
   -55   -982    215   -982 
  -982   -982    192      4 
  -982    251   -982   -982 
  -154     34    166   -154 
  -982    234   -982   -154 
   162   -982   -982   -982 
  -982   -982   -982    162 
   104   -982   -982      4 
  -154   -982    215   -154 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.9e-017 
 0.000000  0.000000  1.000000  0.000000 
 0.111111  0.222222  0.555556  0.111111 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.555556  0.333333  0.111111  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.000000  0.888889  0.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  0.000000  1.000000 
 0.111111  0.222222  0.000000  0.666667 
 0.555556  0.222222  0.000000  0.222222 
 0.222222  0.000000  0.777778  0.000000 
 0.000000  0.000000  0.666667  0.333333 
 0.000000  1.000000  0.000000  0.000000 
 0.111111  0.222222  0.555556  0.111111 
 0.000000  0.888889  0.000000  0.111111 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.666667  0.000000  0.000000  0.333333 
 0.111111  0.000000  0.777778  0.111111 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
G[GC]TG[AC]CGTT[TC][ACT][GA][GT]C[GC]CAT[AT]G
--------------------------------------------------------------------------------




Time 20.03 secs.

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


********************************************************************************
MOTIF  4	width =   15   sites =   9   llr = 142   E-value = 2.9e-008
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  ::::9:::::8::::
pos.-specific     C  a8:::11:89:899:
probability       G  :::::1:::::11:2
matrix            T  :2aa189a2121:18

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

Multilevel           CCTTATTTCCACCCT
consensus             T      T T   G
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
WashU_Skud_Contig1850.5      +    723  6.31e-10 TATTGTTCAC CCTTATTTCCACCCT CAAAGGATAA
MIT_Sbay_c841_3215           +    742  6.31e-10 TATTGTTCAC CCTTATTTCCACCCT CAAACGACAA
MIT_Smik_c193_2483           +    716  6.31e-10 TATTATTCAC CCTTATTTCCACCCT CAAACGATAA
MIT_Spar_c429_3020           +    716  6.31e-10 TATTGTTCAC CCTTATTTCCACCCT CAAACGATAA
SGD_Scer_YDL205C             +    715  6.31e-10 TATTGTTCAC CCTTATTTCCACCCT CAAACGATAA
MIT_Spar_c130_3923           -    332  8.79e-08 AACAACATAT CCTTAGCTTCACCCT GCCAATACTG
MIT_Sbay_c896_21277          +    178  6.08e-07 AAAATTGTTT CTTTATTTTTTCCCT CTTTTCCATG
SGD_Scer_YDR047W             -    467  1.01e-06 GAAAAAACTT CTTTACTTCCATGCG CGCGTTTTTG
WashU_Skud_Contig1362.1      +    186  1.07e-06 AATTTTTTGG CCTTTTTTCCTGCTG CCAAAAAACC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Skud_Contig1850.5           6.3e-10  722_[+4]_123
MIT_Sbay_c841_3215                6.3e-10  741_[+4]_104
MIT_Smik_c193_2483                6.3e-10  715_[+4]_130
MIT_Spar_c429_3020                6.3e-10  715_[+4]_130
SGD_Scer_YDL205C                  6.3e-10  714_[+4]_131
MIT_Spar_c130_3923                8.8e-08  331_[-4]_654
MIT_Sbay_c896_21277               6.1e-07  177_[+4]_808
SGD_Scer_YDR047W                    1e-06  466_[-4]_519
WashU_Skud_Contig1362.1           1.1e-06  185_[+4]_561
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=15 seqs=9
WashU_Skud_Contig1850.5  (  723) CCTTATTTCCACCCT  1 
MIT_Sbay_c841_3215       (  742) CCTTATTTCCACCCT  1 
MIT_Smik_c193_2483       (  716) CCTTATTTCCACCCT  1 
MIT_Spar_c429_3020       (  716) CCTTATTTCCACCCT  1 
SGD_Scer_YDL205C         (  715) CCTTATTTCCACCCT  1 
MIT_Spar_c130_3923       (  332) CCTTAGCTTCACCCT  1 
MIT_Sbay_c896_21277      (  178) CTTTATTTTTTCCCT  1 
SGD_Scer_YDR047W         (  467) CTTTACTTCCATGCG  1 
WashU_Skud_Contig1362.1  (  186) CCTTTTTTCCTGCTG  1 
//

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

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 7935 bayes= 9.78245 E= 2.9e-008 
  -982    251   -982   -982 
  -982    215   -982    -55 
  -982   -982   -982    162 
  -982   -982   -982    162 
   145   -982   -982   -154 
  -982    -66    -66    126 
  -982    -66   -982    145 
  -982   -982   -982    162 
  -982    215   -982    -55 
  -982    234   -982   -154 
   126   -982   -982    -55 
  -982    215    -66   -154 
  -982    234    -66   -982 
  -982    234   -982   -154 
  -982   -982     34    126 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 2.9e-008 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.888889  0.000000  0.000000  0.111111 
 0.000000  0.111111  0.111111  0.777778 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.777778  0.000000  0.222222 
 0.000000  0.888889  0.000000  0.111111 
 0.777778  0.000000  0.000000  0.222222 
 0.000000  0.777778  0.111111  0.111111 
 0.000000  0.888889  0.111111  0.000000 
 0.000000  0.888889  0.000000  0.111111 
 0.000000  0.000000  0.222222  0.777778 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
C[CT]TTATTT[CT]C[AT]CCC[TG]
--------------------------------------------------------------------------------




Time 26.29 secs.

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


********************************************************************************
MOTIF  5	width =   20   sites =   9   llr = 161   E-value = 2.9e-008
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  2:6197:7:::::::22:a6
pos.-specific     C  :8211:6:11:9:1:::6:3
probability       G  8228:2:3:6:196:88::1
matrix            T  :::::14:93a:13a::4::

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

Multilevel           GCAGAACATGTCGGTGGCAA
consensus            AGC  GTG T   T AAT C
sequence               G                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
SGD_Scer_YDL205C             +    561  1.62e-11 AAGGGTAGCA GCAGAATGTGTCGGTGGTAC CGGTGTGATA
MIT_Spar_c130_3923           +    171  4.79e-11 GACAAAAAGG GCAGAACATTTCGTTGGCAA AATTTAAACT
SGD_Scer_YDR047W             +    174  1.01e-10 GATGAAAATG GCAGAACATTTCGCTGGCAA AATTAAAACT
WashU_Skud_Contig1850.5      +    566  1.81e-09 AAGGATAGCA ACGGAATGTGTCGGTGGTAG CGGATGTGGC
MIT_Smik_c193_2483           +    563  3.96e-09 AAGGGTAGCG ACGGCGTATGTCGGTGGTAC CGGATATGGC
WashU_Skud_Contig1362.1      +    138  5.96e-09 CATACGAAAG GCAGAACACCTCGTTGACAA AACTGAAACT
MIT_Sbay_c841_3215           +    572  1.26e-08 CGAGGGTCGC GGCCAATGTGTCGGTAGTAC CGGATGGGGC
MIT_Sbay_c896_21277          +    144  3.29e-08 GACACGAATA GGAAAGCATTTCGTTGACAA AAATAAAATT
MIT_Spar_c429_3020           +    786  4.67e-08 GGATTGAAAA GCCGATCATGTGTGTAGCAA TAGTAGTAGT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDL205C                  1.6e-11  560_[+5]_280
MIT_Spar_c130_3923                4.8e-11  170_[+5]_810
SGD_Scer_YDR047W                    1e-10  173_[+5]_807
WashU_Skud_Contig1850.5           1.8e-09  565_[+5]_275
MIT_Smik_c193_2483                  4e-09  562_[+5]_278
WashU_Skud_Contig1362.1             6e-09  137_[+5]_604
MIT_Sbay_c841_3215                1.3e-08  571_[+5]_269
MIT_Sbay_c896_21277               3.3e-08  143_[+5]_837
MIT_Spar_c429_3020                4.7e-08  785_[+5]_55
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=9
SGD_Scer_YDL205C         (  561) GCAGAATGTGTCGGTGGTAC  1 
MIT_Spar_c130_3923       (  171) GCAGAACATTTCGTTGGCAA  1 
SGD_Scer_YDR047W         (  174) GCAGAACATTTCGCTGGCAA  1 
WashU_Skud_Contig1850.5  (  566) ACGGAATGTGTCGGTGGTAG  1 
MIT_Smik_c193_2483       (  563) ACGGCGTATGTCGGTGGTAC  1 
WashU_Skud_Contig1362.1  (  138) GCAGAACACCTCGTTGACAA  1 
MIT_Sbay_c841_3215       (  572) GGCCAATGTGTCGGTAGTAC  1 
MIT_Sbay_c896_21277      (  144) GGAAAGCATTTCGTTGACAA  1 
MIT_Spar_c429_3020       (  786) GCCGATCATGTGTGTAGCAA  1 
//

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

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7890 bayes= 9.77424 E= 2.9e-008 
   -55   -982    215   -982 
  -982    215     34   -982 
    78     34     34   -982 
  -154    -66    215   -982 
   145    -66   -982   -982 
   104   -982     34   -154 
  -982    166   -982     45 
   104   -982     92   -982 
  -982    -66   -982    145 
  -982    -66    166      4 
  -982   -982   -982    162 
  -982    234    -66   -982 
  -982   -982    234   -154 
  -982    -66    166      4 
  -982   -982   -982    162 
   -55   -982    215   -982 
   -55   -982    215   -982 
  -982    166   -982     45 
   162   -982   -982   -982 
    78     92    -66   -982 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.9e-008 
 0.222222  0.000000  0.777778  0.000000 
 0.000000  0.777778  0.222222  0.000000 
 0.555556  0.222222  0.222222  0.000000 
 0.111111  0.111111  0.777778  0.000000 
 0.888889  0.111111  0.000000  0.000000 
 0.666667  0.000000  0.222222  0.111111 
 0.000000  0.555556  0.000000  0.444444 
 0.666667  0.000000  0.333333  0.000000 
 0.000000  0.111111  0.000000  0.888889 
 0.000000  0.111111  0.555556  0.333333 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.888889  0.111111  0.000000 
 0.000000  0.000000  0.888889  0.111111 
 0.000000  0.111111  0.555556  0.333333 
 0.000000  0.000000  0.000000  1.000000 
 0.222222  0.000000  0.777778  0.000000 
 0.222222  0.000000  0.777778  0.000000 
 0.000000  0.555556  0.000000  0.444444 
 1.000000  0.000000  0.000000  0.000000 
 0.555556  0.333333  0.111111  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
[GA][CG][ACG]GA[AG][CT][AG]T[GT]TCG[GT]T[GA][GA][CT]A[AC]
--------------------------------------------------------------------------------




Time 32.47 secs.

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


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

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDL205C                 6.46e-34  110_[+1(1.67e-11)]_358_[+2(3.06e-13)]_52_[+5(1.62e-11)]_92_[+3(3.00e-13)]_22_[+4(6.31e-10)]_54_[+5(2.69e-05)]_57
MIT_Spar_c429_3020               3.43e-29  110_[+1(1.67e-11)]_173_[-4(1.29e-05)]_174_[+2(9.57e-12)]_49_[+5(9.46e-05)]_92_[+3(3.00e-13)]_22_[+4(6.31e-10)]_55_[+5(4.67e-08)]_55
MIT_Smik_c193_2483               1.01e-24  112_[+1(1.63e-10)]_21_[-3(6.96e-05)]_319_[+2(1.25e-09)]_50_[+5(3.96e-09)]_91_[+3(1.45e-10)]_22_[+4(6.31e-10)]_130
MIT_Sbay_c841_3215               6.11e-27  39_[+4(6.88e-05)]_57_[+1(5.77e-11)]_371_[+2(2.31e-11)]_49_[+5(1.26e-08)]_108_[+3(3.16e-11)]_22_[+4(6.31e-10)]_104
WashU_Skud_Contig1850.5          2.40e-28  110_[+1(5.77e-11)]_272_[-3(9.23e-05)]_71_[+2(5.55e-10)]_52_[+5(1.81e-09)]_53_[-1(8.53e-05)]_22_[+3(3.00e-13)]_22_[+4(6.31e-10)]_123
SGD_Scer_YDR047W                 4.48e-22  173_[+5(1.01e-10)]_44_[+1(7.68e-10)]_31_[-2(1.18e-09)]_158_[-4(1.01e-06)]_134_[+2(4.56e-05)]_77_[+3(2.43e-10)]_268
MIT_Spar_c130_3923               3.62e-24  22_[+4(6.45e-05)]_133_[+5(4.79e-11)]_44_[+1(4.70e-10)]_32_[-2(2.77e-10)]_25_[-4(8.79e-08)]_124_[-1(9.89e-05)]_222_[+3(2.43e-10)]_36_[+4(1.03e-05)]_143_[+2(2.11e-05)]_54
MIT_Sbay_c896_21277              4.53e-19  143_[+5(3.29e-08)]_14_[+4(6.08e-07)]_13_[+1(2.60e-10)]_13_[-2(1.64e-10)]_493_[+2(7.81e-05)]_197_[-3(4.38e-08)]_12
WashU_Skud_Contig1362.1          3.15e-19  137_[+5(5.96e-09)]_28_[+4(1.07e-06)]_[+1(9.83e-10)]_25_[-2(6.00e-10)]_252_[-2(2.11e-05)]_165_[+3(2.69e-08)]_39
--------------------------------------------------------------------------------

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


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

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

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