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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= HEM12-HEM13.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
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  
SGD_Scer_YDR044W         1.0000   1000  MIT_Spar_c130_3912       1.0000   1000  
MIT_Sbay_c896_21290      1.0000   1000  WashU_Smik_Contig2283.3  1.0000   1000  
********************************************************************************

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

command: meme HEM12-HEM13.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=        8    maxsites=        8    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            7761    N=               8
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.291 C 0.209 G 0.209 T 0.291 
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 =   8   llr = 167   E-value = 1.0e-013
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :1165:9:1a::11:::1a:
pos.-specific     C  :::::a::4:3::11:5:::
probability       G  :9945:1:::1:98:559:a
matrix            T  a::::::a5:6a::95::::

         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           TGGAACATTATTGGTGCGAG
consensus               GG   C C    TG   
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c130_3912           +    244  1.31e-12 TGGTTCAAGC TGGGGCATTATTGGTGGGAG AAGCCAGAAA
MIT_Sbay_c896_21290          +    250  2.00e-11 AGGTCCAAGC TGGGGCATAATTGGTGGGAG AAGCCAGAAA
SGD_Scer_YDR044W             +    252  2.47e-11 TTGTTCAAGC TGGAGCGTTATTGGTGGGAG AACCAGAAAA
WashU_Smik_Contig2283.3      +    240  7.53e-11 TGGTTGAAGC TGGGGCATTATTGGTGGAAG AAGCCAGAAA
WashU_Skud_Contig1362.1      +    101  2.45e-10 TTCTTTCGTT TGGAACATTACTGCTTCGAG CAATAAACAT
MIT_Spar_c130_3923           +    134  5.96e-10 CCACTTCGTT TGAAACATCAGTGGTTCGAG CAGTAATGAC
MIT_Sbay_c896_21277          +    107  7.56e-10 CTAAGTTCTT TAGAACATCATTGGCTCGAG CATTAGTGAC
SGD_Scer_YDR047W             +    137  1.93e-09 TACCTTCGTC TGGAACATCACTAATTCGAG CGGTAAAGAT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c130_3912                1.3e-12  243_[+1]_737
MIT_Sbay_c896_21290                 2e-11  249_[+1]_731
SGD_Scer_YDR044W                  2.5e-11  251_[+1]_729
WashU_Smik_Contig2283.3           7.5e-11  239_[+1]_741
WashU_Skud_Contig1362.1           2.5e-10  100_[+1]_641
MIT_Spar_c130_3923                  6e-10  133_[+1]_847
MIT_Sbay_c896_21277               7.6e-10  106_[+1]_874
SGD_Scer_YDR047W                  1.9e-09  136_[+1]_844
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=20 seqs=8
MIT_Spar_c130_3912       (  244) TGGGGCATTATTGGTGGGAG  1 
MIT_Sbay_c896_21290      (  250) TGGGGCATAATTGGTGGGAG  1 
SGD_Scer_YDR044W         (  252) TGGAGCGTTATTGGTGGGAG  1 
WashU_Smik_Contig2283.3  (  240) TGGGGCATTATTGGTGGAAG  1 
WashU_Skud_Contig1362.1  (  101) TGGAACATTACTGCTTCGAG  1 
MIT_Spar_c130_3923       (  134) TGAAACATCAGTGGTTCGAG  1 
MIT_Sbay_c896_21277      (  107) TAGAACATCATTGGCTCGAG  1 
SGD_Scer_YDR047W         (  137) TGGAACATCACTAATTCGAG  1 
//

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

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7609 bayes= 9.89197 E= 1.0e-013 
  -965   -965   -965    162 
  -137   -965    232   -965 
  -137   -965    232   -965 
    95   -965    109   -965 
    62   -965    151   -965 
  -965    251   -965   -965 
   143   -965    -49   -965 
  -965   -965   -965    162 
  -137    109   -965     62 
   162   -965   -965   -965 
  -965     51    -49     95 
  -965   -965   -965    162 
  -137   -965    232   -965 
  -137    -49    209   -965 
  -965    -49   -965    143 
  -965   -965    151     62 
  -965    151    151   -965 
  -137   -965    232   -965 
   162   -965   -965   -965 
  -965   -965    251   -965 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 1.0e-013 
 0.000000  0.000000  0.000000  1.000000 
 0.125000  0.000000  0.875000  0.000000 
 0.125000  0.000000  0.875000  0.000000 
 0.625000  0.000000  0.375000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.875000  0.000000  0.125000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.125000  0.375000  0.000000  0.500000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.250000  0.125000  0.625000 
 0.000000  0.000000  0.000000  1.000000 
 0.125000  0.000000  0.875000  0.000000 
 0.125000  0.125000  0.750000  0.000000 
 0.000000  0.125000  0.000000  0.875000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  0.500000  0.500000  0.000000 
 0.125000  0.000000  0.875000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 regular expression
--------------------------------------------------------------------------------
TGG[AG][AG]CAT[TC]A[TC]TGGT[GT][CG]GAG
--------------------------------------------------------------------------------




Time  6.16 secs.

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


********************************************************************************
MOTIF  2	width =   20   sites =   8   llr = 161   E-value = 5.1e-011
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  ::1:1::1:6:1:::1:98a
pos.-specific     C  1::951:9::a:85:3::::
probability       G  9:4:4:a:a4::154:513:
matrix            T  :a51:9:::::91:665:::

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

Multilevel           GTTCCTGCGACTCCTTGAAA
consensus              G G    G   GGCT G 
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
WashU_Smik_Contig2283.3      +    313  1.96e-11 TTGGTTTCGG GTTCCTGCGACTCGTTTAAA AAAGAAAAGG
MIT_Sbay_c896_21290          +    316  1.96e-11 AATGGCTTCG GTTCCTGCGACTCGTTTAAA AAGAAAAGGG
MIT_Spar_c130_3912           +    310  1.96e-11 TTTGGATTCT GTTCCTGCGACTCGTTTAAA AGAAGAAGGG
SGD_Scer_YDR044W             +    317  1.96e-11 TTTGGCTTCT GTTCCTGCGACTCGTTTAAA AGTAGAAGGG
SGD_Scer_YDR047W             +    871  6.56e-11 TAATGTAGCC GTGCATGCGGCTCCGCGAAA AGAGCTCTGC
MIT_Spar_c130_3923           +    880  1.43e-10 TTATATAGCC GTACGTGCGGCTCCTCGAGA AAGGCCCTGC
WashU_Skud_Contig1362.1      -    420  9.20e-09 GAAGGTGGCA CTGCGTGAGACTGCGTGGAA AGTATAAATA
MIT_Sbay_c896_21277          +    841  2.90e-08 TTTTATAGCC GTGTGCGCGGCATCGAGAGA CAGGTTCAGC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
WashU_Smik_Contig2283.3             2e-11  312_[+2]_668
MIT_Sbay_c896_21290                 2e-11  315_[+2]_665
MIT_Spar_c130_3912                  2e-11  309_[+2]_671
SGD_Scer_YDR044W                    2e-11  316_[+2]_664
SGD_Scer_YDR047W                  6.6e-11  870_[+2]_110
MIT_Spar_c130_3923                1.4e-10  879_[+2]_101
WashU_Skud_Contig1362.1           9.2e-09  419_[-2]_322
MIT_Sbay_c896_21277               2.9e-08  840_[+2]_140
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=20 seqs=8
WashU_Smik_Contig2283.3  (  313) GTTCCTGCGACTCGTTTAAA  1 
MIT_Sbay_c896_21290      (  316) GTTCCTGCGACTCGTTTAAA  1 
MIT_Spar_c130_3912       (  310) GTTCCTGCGACTCGTTTAAA  1 
SGD_Scer_YDR044W         (  317) GTTCCTGCGACTCGTTTAAA  1 
SGD_Scer_YDR047W         (  871) GTGCATGCGGCTCCGCGAAA  1 
MIT_Spar_c130_3923       (  880) GTACGTGCGGCTCCTCGAGA  1 
WashU_Skud_Contig1362.1  (  420) CTGCGTGAGACTGCGTGGAA  1 
MIT_Sbay_c896_21277      (  841) GTGTGCGCGGCATCGAGAGA  1 
//

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

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7609 bayes= 9.89197 E= 5.1e-011 
  -965    -49    232   -965 
  -965   -965   -965    162 
  -137   -965    109     62 
  -965    232   -965   -137 
  -137    151    109   -965 
  -965    -49   -965    143 
  -965   -965    251   -965 
  -137    232   -965   -965 
  -965   -965    251   -965 
    95   -965    109   -965 
  -965    251   -965   -965 
  -137   -965   -965    143 
  -965    209    -49   -137 
  -965    151    151   -965 
  -965   -965    109     95 
  -137     51   -965     95 
  -965   -965    151     62 
   143   -965    -49   -965 
   121   -965     51   -965 
   162   -965   -965   -965 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 5.1e-011 
 0.000000  0.125000  0.875000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.125000  0.000000  0.375000  0.500000 
 0.000000  0.875000  0.000000  0.125000 
 0.125000  0.500000  0.375000  0.000000 
 0.000000  0.125000  0.000000  0.875000 
 0.000000  0.000000  1.000000  0.000000 
 0.125000  0.875000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.625000  0.000000  0.375000  0.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.125000  0.000000  0.000000  0.875000 
 0.000000  0.750000  0.125000  0.125000 
 0.000000  0.500000  0.500000  0.000000 
 0.000000  0.000000  0.375000  0.625000 
 0.125000  0.250000  0.000000  0.625000 
 0.000000  0.000000  0.500000  0.500000 
 0.875000  0.000000  0.125000  0.000000 
 0.750000  0.000000  0.250000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 regular expression
--------------------------------------------------------------------------------
GT[TG]C[CG]TGCG[AG]CTC[CG][TG][TC][GT]A[AG]A
--------------------------------------------------------------------------------




Time 12.22 secs.

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


********************************************************************************
MOTIF  3	width =   15   sites =   8   llr = 136   E-value = 3.8e-008
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  :9::6:::::1::::
pos.-specific     C  5::::::5:5:::4:
probability       G  519a4:::a59a5::
matrix            T  ::1::aa5::::56a

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

Multilevel           CAGGATTCGCGGGTT
consensus            G   G  T G  TC 
sequence                            
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
SGD_Scer_YDR044W             +    623  5.51e-09 ACAAACTCCA GAGGATTTGCGGGCT TGATGATAAA
MIT_Sbay_c896_21277          -    211  5.51e-09 CTCGTTTATA CAGGGTTCGGGGTTT TTTGACGCCA
MIT_Spar_c130_3923           -    240  5.51e-09 ATATACGGGA CAGGGTTCGGGGTTT TGGTGGCAGG
SGD_Scer_YDR047W             -    243  5.51e-09 ATATACAGGA CAGGGTTCGGGGTTT TTGGCGGCAG
WashU_Smik_Contig2283.3      +    624  8.25e-09 TGAACTTCTT GAGGATTTGCGGGTT CGGTGATAAA
MIT_Sbay_c896_21290          +    622  1.72e-08 CGGAACTCTT GGGGATTTGCGGGCT CGCTAATAAA
MIT_Spar_c130_3912           +    618  4.23e-08 CGAAACTCTA GAGGATTTGCAGGCT CGGTGATAAA
WashU_Skud_Contig1362.1      -    206  5.24e-08 CTCGCTTCTA CATGATTCGGGGTTT TTTGGCAGCA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR044W                  5.5e-09  622_[+3]_363
MIT_Sbay_c896_21277               5.5e-09  210_[-3]_775
MIT_Spar_c130_3923                5.5e-09  239_[-3]_746
SGD_Scer_YDR047W                  5.5e-09  242_[-3]_743
WashU_Smik_Contig2283.3           8.2e-09  623_[+3]_362
MIT_Sbay_c896_21290               1.7e-08  621_[+3]_364
MIT_Spar_c130_3912                4.2e-08  617_[+3]_368
WashU_Skud_Contig1362.1           5.2e-08  205_[-3]_541
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=15 seqs=8
SGD_Scer_YDR044W         (  623) GAGGATTTGCGGGCT  1 
MIT_Sbay_c896_21277      (  211) CAGGGTTCGGGGTTT  1 
MIT_Spar_c130_3923       (  240) CAGGGTTCGGGGTTT  1 
SGD_Scer_YDR047W         (  243) CAGGGTTCGGGGTTT  1 
WashU_Smik_Contig2283.3  (  624) GAGGATTTGCGGGTT  1 
MIT_Sbay_c896_21290      (  622) GGGGATTTGCGGGCT  1 
MIT_Spar_c130_3912       (  618) GAGGATTTGCAGGCT  1 
WashU_Skud_Contig1362.1  (  206) CATGATTCGGGGTTT  1 
//

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

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 15 n= 7649 bayes= 9.89955 E= 3.8e-008 
  -965    151    151   -965 
   143   -965    -49   -965 
  -965   -965    232   -137 
  -965   -965    251   -965 
    95   -965    109   -965 
  -965   -965   -965    162 
  -965   -965   -965    162 
  -965    151   -965     62 
  -965   -965    251   -965 
  -965    151    151   -965 
  -137   -965    232   -965 
  -965   -965    251   -965 
  -965   -965    151     62 
  -965    109   -965     95 
  -965   -965   -965    162 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 15 nsites= 8 E= 3.8e-008 
 0.000000  0.500000  0.500000  0.000000 
 0.875000  0.000000  0.125000  0.000000 
 0.000000  0.000000  0.875000  0.125000 
 0.000000  0.000000  1.000000  0.000000 
 0.625000  0.000000  0.375000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.125000  0.000000  0.875000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.000000  0.500000  0.500000 
 0.000000  0.375000  0.000000  0.625000 
 0.000000  0.000000  0.000000  1.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 regular expression
--------------------------------------------------------------------------------
[CG]AGG[AG]TT[CT]G[CG]GG[GT][TC]T
--------------------------------------------------------------------------------




Time 18.15 secs.

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


********************************************************************************
MOTIF  4	width =   20   sites =   8   llr = 155   E-value = 1.1e-008
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  aa13::a6a415:5::::1:
pos.-specific     C  ::::54::::9:111a:1:4
probability       G  ::5856:4:6:5::4:a::6
matrix            T  ::4:::::::::945::99:

         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           AAGGCGAAAGCATATCGTTG
consensus              TAGC G A G TG    C
sequence                                 
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c130_3912           +    273  3.90e-12 GAAGCCAGAA AAGGCGAAAGCGTAGCGTTC TTTGAAATTT
SGD_Scer_YDR044W             +    280  3.90e-12 AGAACCAGAA AAGGCGAAAGCGTAGCGTTC TTTGAAATTT
MIT_Sbay_c896_21290          +    279  2.45e-10 GAAGCCAGAA AATGCGAAAGCGTACCGTTC TGTGAAAAAT
MIT_Spar_c130_3923           +    167  3.43e-10 TAATGACAAA AAGGGCAGAACATTTCGTTG GCAAAATTTA
MIT_Sbay_c896_21277          +    140  1.28e-09 TAGTGACACG AATAGGAAAGCATTTCGTTG ACAAAAATAA
SGD_Scer_YDR047W             +    170  3.28e-09 TAAAGATGAA AATGGCAGAACATTTCGCTG GCAAAATTAA
WashU_Smik_Contig2283.3      +    269  7.13e-09 GAAGCCAGAA AAGACGAAAGAGTAGCGTAG CGTTCTTTCA
WashU_Skud_Contig1362.1      +    134  8.94e-09 TAAACATACG AAAGGCAGAACACCTCGTTG ACAAAACTGA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c130_3912                3.9e-12  272_[+4]_708
SGD_Scer_YDR044W                  3.9e-12  279_[+4]_701
MIT_Sbay_c896_21290               2.4e-10  278_[+4]_702
MIT_Spar_c130_3923                3.4e-10  166_[+4]_814
MIT_Sbay_c896_21277               1.3e-09  139_[+4]_841
SGD_Scer_YDR047W                  3.3e-09  169_[+4]_811
WashU_Smik_Contig2283.3           7.1e-09  268_[+4]_712
WashU_Skud_Contig1362.1           8.9e-09  133_[+4]_608
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=20 seqs=8
MIT_Spar_c130_3912       (  273) AAGGCGAAAGCGTAGCGTTC  1 
SGD_Scer_YDR044W         (  280) AAGGCGAAAGCGTAGCGTTC  1 
MIT_Sbay_c896_21290      (  279) AATGCGAAAGCGTACCGTTC  1 
MIT_Spar_c130_3923       (  167) AAGGGCAGAACATTTCGTTG  1 
MIT_Sbay_c896_21277      (  140) AATAGGAAAGCATTTCGTTG  1 
SGD_Scer_YDR047W         (  170) AATGGCAGAACATTTCGCTG  1 
WashU_Smik_Contig2283.3  (  269) AAGACGAAAGAGTAGCGTAG  1 
WashU_Skud_Contig1362.1  (  134) AAAGGCAGAACACCTCGTTG  1 
//

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

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7609 bayes= 9.89197 E= 1.1e-008 
   162   -965   -965   -965 
   162   -965   -965   -965 
  -137   -965    151     21 
   -38   -965    209   -965 
  -965    151    151   -965 
  -965    109    183   -965 
   162   -965   -965   -965 
    95   -965    109   -965 
   162   -965   -965   -965 
    21   -965    183   -965 
  -137    232   -965   -965 
    62   -965    151   -965 
  -965    -49   -965    143 
    62    -49   -965     21 
  -965    -49    109     62 
  -965    251   -965   -965 
  -965   -965    251   -965 
  -965    -49   -965    143 
  -137   -965   -965    143 
  -965    109    183   -965 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 1.1e-008 
 1.000000  0.000000  0.000000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.125000  0.000000  0.500000  0.375000 
 0.250000  0.000000  0.750000  0.000000 
 0.000000  0.500000  0.500000  0.000000 
 0.000000  0.375000  0.625000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.625000  0.000000  0.375000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.375000  0.000000  0.625000  0.000000 
 0.125000  0.875000  0.000000  0.000000 
 0.500000  0.000000  0.500000  0.000000 
 0.000000  0.125000  0.000000  0.875000 
 0.500000  0.125000  0.000000  0.375000 
 0.000000  0.125000  0.375000  0.500000 
 0.000000  1.000000  0.000000  0.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.000000  0.125000  0.000000  0.875000 
 0.125000  0.000000  0.000000  0.875000 
 0.000000  0.375000  0.625000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 regular expression
--------------------------------------------------------------------------------
AA[GT][GA][CG][GC]A[AG]A[GA]C[AG]T[AT][TG]CGTT[GC]
--------------------------------------------------------------------------------




Time 24.05 secs.

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


********************************************************************************
MOTIF  5	width =   20   sites =   8   llr = 150   E-value = 3.2e-007
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  1::::1a643:6:85:aa::
pos.-specific     C  135:a:::44:4:11a::31
probability       G  :1:::9:431a:91:::::9
matrix            T  865a:::::3::1:4:::8:

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

Multilevel           TTCTCGAAACGAGAACAATG
consensus             CT    GCA C  T   C 
sequence                     GT          
                                         
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                    Site      
-------------            ------  ----- ---------            --------------------
MIT_Spar_c130_3912           +    160  8.41e-11 TTATATAGCC TTTTCGAAACGAGAACAATG GACAAATCAA
MIT_Sbay_c896_21290          +    166  1.14e-10 TTATATAGCT TTCTCGAAGGGAGAACAATG GATAAATCAA
MIT_Spar_c130_3923           +    927  2.25e-10 CACTAGCTGA TCCTCGAGCTGCGATCAACG AAAGCCCCAT
SGD_Scer_YDR044W             +    164  6.26e-10 CTTATATAGC CTTTCGAAACGAGAACAATG GGCAAAGCAA
MIT_Sbay_c896_21277          +    888  1.02e-09 ATTTGCCTAA TTCTCGAGCTGAGGCCAATG AAGGCAGCTT
SGD_Scer_YDR047W             +    918  1.45e-09 CTCTACCTGA ACTTCGAGCCGCGATCAACG AAAGCTCTCA
WashU_Smik_Contig2283.3      +    156  6.02e-09 TTATATAGCC TTTTCAAAAAGAGAACAATG GTCAAATAAA
WashU_Skud_Contig1362.1      +    363  3.46e-08 AATTTGCTAA TGCTCGAAGAGCTCTCAATC AATCACCCAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
MIT_Spar_c130_3912                8.4e-11  159_[+5]_821
MIT_Sbay_c896_21290               1.1e-10  165_[+5]_815
MIT_Spar_c130_3923                2.2e-10  926_[+5]_54
SGD_Scer_YDR044W                  6.3e-10  163_[+5]_817
MIT_Sbay_c896_21277                 1e-09  887_[+5]_93
SGD_Scer_YDR047W                  1.4e-09  917_[+5]_63
WashU_Smik_Contig2283.3             6e-09  155_[+5]_825
WashU_Skud_Contig1362.1           3.5e-08  362_[+5]_379
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=20 seqs=8
MIT_Spar_c130_3912       (  160) TTTTCGAAACGAGAACAATG  1 
MIT_Sbay_c896_21290      (  166) TTCTCGAAGGGAGAACAATG  1 
MIT_Spar_c130_3923       (  927) TCCTCGAGCTGCGATCAACG  1 
SGD_Scer_YDR044W         (  164) CTTTCGAAACGAGAACAATG  1 
MIT_Sbay_c896_21277      (  888) TTCTCGAGCTGAGGCCAATG  1 
SGD_Scer_YDR047W         (  918) ACTTCGAGCCGCGATCAACG  1 
WashU_Smik_Contig2283.3  (  156) TTTTCAAAAAGAGAACAATG  1 
WashU_Skud_Contig1362.1  (  363) TGCTCGAAGAGCTCTCAATC  1 
//

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

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 20 n= 7609 bayes= 9.89197 E= 3.2e-007 
  -137    -49   -965    121 
  -965     51    -49     95 
  -965    151   -965     62 
  -965   -965   -965    162 
  -965    251   -965   -965 
  -137   -965    232   -965 
   162   -965   -965   -965 
    95   -965    109   -965 
    21    109     51   -965 
   -38    109    -49    -38 
  -965   -965    251   -965 
    95    109   -965   -965 
  -965   -965    232   -137 
   121    -49    -49   -965 
    62    -49   -965     21 
  -965    251   -965   -965 
   162   -965   -965   -965 
   162   -965   -965   -965 
  -965     51   -965    121 
  -965    -49    232   -965 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 20 nsites= 8 E= 3.2e-007 
 0.125000  0.125000  0.000000  0.750000 
 0.000000  0.250000  0.125000  0.625000 
 0.000000  0.500000  0.000000  0.500000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  1.000000  0.000000  0.000000 
 0.125000  0.000000  0.875000  0.000000 
 1.000000  0.000000  0.000000  0.000000 
 0.625000  0.000000  0.375000  0.000000 
 0.375000  0.375000  0.250000  0.000000 
 0.250000  0.375000  0.125000  0.250000 
 0.000000  0.000000  1.000000  0.000000 
 0.625000  0.375000  0.000000  0.000000 
 0.000000  0.000000  0.875000  0.125000 
 0.750000  0.125000  0.125000  0.000000 
 0.500000  0.125000  0.000000  0.375000 
 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  0.250000  0.000000  0.750000 
 0.000000  0.125000  0.875000  0.000000 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 regular expression
--------------------------------------------------------------------------------
T[TC][CT]TCGA[AG][ACG][CAT]G[AC]GA[AT]CAA[TC]G
--------------------------------------------------------------------------------




Time 29.84 secs.

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


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

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
SGD_Scer_YDR047W                 7.45e-23  50_[+5(5.03e-05)]_66_[+1(1.93e-09)]_13_[+4(3.28e-09)]_53_[-3(5.51e-09)]_613_[+2(6.56e-11)]_27_[+5(1.45e-09)]_63
MIT_Spar_c130_3923               1.06e-24  133_[+1(5.96e-10)]_13_[+4(3.43e-10)]_53_[-3(5.51e-09)]_110_[-4(7.03e-05)]_238_[+1(6.23e-05)]_237_[+2(1.43e-10)]_27_[+5(2.25e-10)]_54
MIT_Sbay_c896_21277              2.78e-21  5_[-4(5.78e-05)]_81_[+1(7.56e-10)]_13_[+4(1.28e-09)]_51_[-3(5.51e-09)]_615_[+2(2.90e-08)]_27_[+5(1.02e-09)]_93
WashU_Skud_Contig1362.1          1.22e-19  100_[+1(2.45e-10)]_13_[+4(8.94e-09)]_52_[-3(5.24e-08)]_142_[+5(3.46e-08)]_37_[-2(9.20e-09)]_322
SGD_Scer_YDR044W                 3.05e-28  163_[+5(6.26e-10)]_68_[+1(2.47e-11)]_8_[+4(3.90e-12)]_17_[+2(1.96e-11)]_286_[+3(5.51e-09)]_363
MIT_Spar_c130_3912               1.93e-29  159_[+5(8.41e-11)]_64_[+1(1.31e-12)]_9_[+4(3.90e-12)]_17_[+2(1.96e-11)]_288_[+3(4.23e-08)]_69_[-4(1.60e-05)]_279
MIT_Sbay_c896_21290              7.41e-27  165_[+5(1.14e-10)]_64_[+1(2.00e-11)]_9_[+4(2.45e-10)]_17_[+2(1.96e-11)]_8_[-3(7.60e-05)]_3_[-4(2.55e-05)]_240_[+3(1.72e-08)]_66_[-4(1.70e-05)]_278
WashU_Smik_Contig2283.3          1.31e-23  7_[+3(8.33e-05)]_39_[-5(9.82e-05)]_74_[+5(6.02e-09)]_64_[+1(7.53e-11)]_9_[+4(7.13e-09)]_24_[+2(1.96e-11)]_61_[-2(3.93e-05)]_88_[+2(7.74e-05)]_102_[+3(8.25e-09)]_362
--------------------------------------------------------------------------------

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


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

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

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