meme.ino_up800.tcm

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MEME - Motif discovery tool
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MEME version 3.5.3 (Release date: 2006-03-08 09:30:25 +1000 (Wed, 08 Mar 2006))

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.
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REFERENCE
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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.
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TRAINING SET
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DATAFILE= /home/tbailey/tests/INO_up800.s
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
CHO1                     1.0000    800  CHO2                     1.0000    800  
FAS1                     1.0000    800  FAS2                     1.0000    800  
ACC1                     1.0000    800  INO1                     1.0000    800  
OPI3                     1.0000    800  
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COMMAND LINE SUMMARY
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This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme /home/tbailey/tests/INO_up800.s -mod tcm -dna -revcomp -bfile /home/tbailey/tests/yeast.nc.6.freq -nostatus -nmotifs 2 

model:  mod=           tcm    nmotifs=         2    evt=           inf
object function=  E-value of product of p-values
width:  minw=            8    maxw=           50    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        2    maxsites=       35    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            5600    N=               7
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.304 C 0.196 G 0.196 T 0.304 
Background letter frequencies (from /home/tbailey/tests/yeast.nc.6.freq):
A 0.324 C 0.176 G 0.176 T 0.324 
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MOTIF  1	width =   15   sites =  14   llr = 174   E-value = 2.3e-003
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--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  :::8:a:::442411
pos.-specific     C  :1a19:117527644
probability       G  :::1:::83:4:11:
matrix            T  a9:11:91:111:44

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

Multilevel           TTCACATGCCACCCC
consensus                    GAGAATT
sequence                       C    
                                    
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value                 Site    
-------------            ------  ----- ---------            ---------------
FAS1                         +     95  6.14e-09 GGCCAAAAAC TTCACATGCCGCCCA GCCAAGCATA
INO1                         -    617  2.63e-08 GACAATACTT TTCACATGCCGCATT TAGCCGCCGA
FAS2                         +    567  1.80e-07 CTCCCGCGTT TTCACATGCTACCTC ATTCGCCTCG
CHO1                         +    611  2.03e-07 ACTTTGAACG TTCACACGGCACCCT CACGCCTTTG
ACC1                         +     83  4.22e-07 CGTTAAAATC TTCACATGGCCCGGC CGCGCGCGCG
CHO2                         +    354  5.33e-07 TGCCACACTT TTCTCATGCCGCATT CATTATTCGC
CHO1                         +    640  7.59e-07 CCTTTGAGCT TTCACATGGACCCAT CTAAAGATGA
INO1                         -    568  8.34e-07 CTCCGCATAT TTCACATTCAACACT TTCGATTCCG
OPI3                         +    637  1.02e-06 CTTTTCAATC TTCATATGCAAACCC ACACATGCAT
INO1                         +    687  1.10e-06 ACTTATTTAA TTCACATGGAGCAGA GAAAGCGCAC
OPI3                         -    582  1.84e-06 GGTGCAACTT TCCACATGCACTCTC ATTGACACCT
INO1                         -    547  2.76e-06 CACTTTCGAT TCCGCATCCAACCCC GGAACACCGG
CHO1                         +    163  3.42e-06 TCTGGCGCCC TTCCCATTCCGAACC ATGTTATATT
CHO2                         -    478  7.37e-06 AATCTGTATT TTCATATGCCTACTT ATAAATTCAC
--------------------------------------------------------------------------------

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	Motif 1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
FAS1                              6.1e-09  94_[+1]_691
INO1                              2.8e-06  546_[-1]_6_[-1]_34_[-1]_55_[+1]_99
FAS2                              1.8e-07  566_[+1]_219
CHO1                              7.6e-07  162_[+1]_433_[+1]_14_[+1]_146
ACC1                              4.2e-07  82_[+1]_703
CHO2                              5.3e-07  353_[+1]_109_[-1]_308
OPI3                                1e-06  581_[-1]_40_[+1]_149
--------------------------------------------------------------------------------

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	Motif 1 in BLOCKS format
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BL   MOTIF 1 width=15 seqs=14
FAS1                     (   95) TTCACATGCCGCCCA  1 
INO1                     (  617) TTCACATGCCGCATT  1 
FAS2                     (  567) TTCACATGCTACCTC  1 
CHO1                     (  611) TTCACACGGCACCCT  1 
ACC1                     (   83) TTCACATGGCCCGGC  1 
CHO2                     (  354) TTCTCATGCCGCATT  1 
CHO1                     (  640) TTCACATGGACCCAT  1 
INO1                     (  568) TTCACATTCAACACT  1 
OPI3                     (  637) TTCATATGCAAACCC  1 
INO1                     (  687) TTCACATGGAGCAGA  1 
OPI3                     (  582) TCCACATGCACTCTC  1 
INO1                     (  547) TCCGCATCCAACCCC  1 
CHO1                     (  163) TTCCCATTCCGAACC  1 
CHO2                     (  478) TTCATATGCCTACTT  1 
//

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	Motif 1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 15 n= 5502 bayes= 8.45817 E= 2.3e-003 
 -1045  -1045  -1045    162 
 -1045    -30  -1045    140 
 -1045    251  -1045  -1045 
   128   -130   -130   -218 
 -1045    229  -1045   -118 
   162  -1045  -1045  -1045 
 -1045   -130  -1045    152 
 -1045   -130    216   -118 
 -1045    202     70  -1045 
    40    151  -1045   -218 
    14     29    102   -218 
   -60    202  -1045   -218 
    14    170   -130  -1045 
  -218    129    -30     14 
  -118    129  -1045     40 
--------------------------------------------------------------------------------

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	Motif 1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 15 nsites= 14 E= 2.3e-003 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.142857  0.000000  0.857143 
 0.000000  1.000000  0.000000  0.000000 
 0.785714  0.071429  0.071429  0.071429 
 0.000000  0.857143  0.000000  0.142857 
 1.000000  0.000000  0.000000  0.000000 
 0.000000  0.071429  0.000000  0.928571 
 0.000000  0.071429  0.785714  0.142857 
 0.000000  0.714286  0.285714  0.000000 
 0.428571  0.500000  0.000000  0.071429 
 0.357143  0.214286  0.357143  0.071429 
 0.214286  0.714286  0.000000  0.071429