MEME -- Multiple EM for Motif Elicitation

Motif discovery tool


MEME sends you three e-mail messages: The e-mail messages are explained in the following sections. A sample MEME results file is also provided

  • Confirmation message

    The first e-mail message you receive should be a confirmation message to let you know that your motif discovery request has been received. You should receive an e-mail message that looks something like this:
    Subject: MEME job 7215957 confirmation: alcohol dehydrogenases (adh.s)
     
    Your MEME request number 7215957 is being processed.
    You should receive two subsequent messages containing:
            1) your MEME results
            2) a MAST analysis of your sequences using the MEME results
    
    Remember to save your MEME results to a file so that you can use the motifs
    to search sequence databases with MAST (http://www.sdsc.edu/MEME).
    

    If you don't receive the confirmation message, check that your email address is correct and reachable from outside your location.

  • MEME Results

    The second e-mail message you should receive contains the results of the MEME analysis of your sequences for shared motifs. Click on the hot-links below to see examples of each type of information that MEME returns. The MEME results consist of:

    For each motif that it discovers in the training set, MEME prints the following information:

  • Mast Results

    The third e-mail message you should receive contains the results of a MAST search of the training set using the motifs found by MEME. This gives several additional ways of viewing how the motifs occur in the training set. You may also want to use the motifs to search one of the large sequence databases available through the MAST website.

  • Sample MEME Results

    Here is an actual MEME results file.


    
    ********************************************************************************
    MEME - Motif discovery tool
    ********************************************************************************
    MEME version 2.0 (Release date: 1996/08/29 00:23:06)
    
    For further information on how to interpret these results or to get
    a copy of the MEME software please access http://www.sdsc.edu/MEME.
    
    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://www.sdsc.edu/MEME.
    ********************************************************************************
    
    
    
    ********************************************************************************
    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
    ********************************************************************************
    Sequence name           Length         Sequence name           Length         
    -------------           ------         -------------           ------         
    2BHD_STREX                 255         3BHD_COMTE                 253         
    ADH_DROME                  255         AP27_MOUSE                 244         
    BA72_EUBSP                 249         BDH_HUMAN                  343         
    BPHB_PSEPS                 275         BUDC_KLETE                 241         
    DHES_HUMAN                 327         DHGB_BACME                 262         
    DHII_HUMAN                 292         DHMA_FLAS1                 270         
    ENTA_ECOLI                 248         FIXR_BRAJA                 278         
    GUTD_ECOLI                 259         HDE_CANTR                  906         
    HDHA_ECOLI                 255         LIGD_PSEPA                 305         
    NODG_RHIME                 245         RIDH_KLEAE                 249         
    YINL_LISMO                 248         YRTP_BACSU                 238         
    CSGA_MYXXA                 166         DHB2_HUMAN                 387         
    DHB3_HUMAN                 310         DHCA_HUMAN                 276         
    FABI_ECOLI                 262         FVT1_HUMAN                 332         
    HMTR_LEIMA                 287         MAS1_AGRRA                 476         
    PCR_PEA                    399         RFBB_NEIGO                 346         
    YURA_MYXXA                 258         
    ********************************************************************************
    
    
    
    ********************************************************************************
    EXPLANATION OF RESULTS
    ********************************************************************************
    For each motif that it discovers in the training set, MEME prints the
    following information:
     
        Summary Line
     
        This line gives the width (`width') and expected number of occurrences in
        the training set (`sites') of the motif. MEME numbers the motifs
        consecutively from one as it finds them. MEME usually finds the most
        statistically significant motifs first. Each motif describes a pattern of a
        fixed width--no gaps are allowed in MEME motifs. MEME estimates
        the number of places the motif occurs in the training set. This need
        not be an integer value.
     
        Simplified Motif Letter-probability Matrix
     
        MEME motifs are represented by letter-probability matrices that
        specify the probability of each possible letter appearing at each
        possible position in an occurrence of the motif. In order to make it
        easier to see which letters are most likely in each of the columns of
        the motif, the simplified motif shows the letter probabilities multiplied
        by 10 rounded to the nearest integer. Zeros are replaced by ":" (the
        colon) for readability.
     
        Information Content Diagram
     
        The information content diagram provides an idea of which positions
        in the motif are most highly conserved. Each column (position) in a
        motif can be characterized by the amount of information it contains
        (measured in bits). Highly conserved positions in the motif have high
        information; positions where all letters are equally likely have low
        information. The diagram is printed so that each column lines up with
        the same column in the simplified motif letter-probability matrix above
        it. Summing the information content for each position in the motif
        gives the total information content of the motif (shown in parentheses
        to the left of the diagram). This gives a measure of the usefulness of
        the motif for database searches. For a motif to be useful for database
        searches, it must as a rule contain at least log_2(N) bits of
        information where N is the number of sequences in the database
        being searched. For example, to effectively search a database
        containing 100,000 sequences for occurrences of a single motif, the
        motif should have an IC of at least 16.6 bits. Motifs with lower
        information content are still useful when a family of sequences shares
        more than one motif since they can be combined in multiple motif
        searches (using MAST).
     
        Multilevel Consensus Sequence
     
        The multilevel consensus sequence corresponding to the motif is an
        aid in remembering and understanding the motif. It is calculated from
        the motif letter-probability matrix as follows. Separately for each
        column of the motif, the letters in the alphabet are sorted in
        decreasing order by the probability with which they are expected to
        occur in that position of motif occurrences. The sorted letters are
        then printed vertically with the most probable letter on top. Only
        letters with probabilities of 0.2 or higher at that position in the motif
        are printed. As an example, the multilevel consensus sequence of
        motif 2 in the sample output is:
     
        Multilevel       LITGAASGIG
        consensus         V  GS
        sequence              G
     
        This multilevel consensus sequence says several things about the
        motif. First, the most likely form of the motif can be read from the top
        line as LITGAASGIG. Second, that only letter L has probability
        more than 0.2 in position 1 of the motif, both I and V have probability
        greater than 0.2 in position 2, etc. Third, a rough approximation of the
        motif can be made by converting the multilevel consensus sequence
        into the Prosite signature
        L-[IV]-T-G-[AG]-[ASG]-S-G-I-G. The multilevel
        consensus sequence is printed so that each column lines up with
        the same column in the simplified motif and information content
        diagrams above it.
     
        Possible Examples of the Motif
     
        As a further aid in understanding the motif, MEME displays a list of
        possible occurrences of the motif in the training set. This list is made
        by converting the motif letter-probability matrix into a
        position-dependent scoring matrix (log-odds matrix) and using that
        to compute a match score between each position in the training set
        and the motif. All positions which score above a threshold score are
        listed. (The threshold score is chosen by MEME such that the
        expected number of non-motif positions listed in error will equal the
        number of actual motif positions not listed.) The format of the list is
        sequence name, starting position of the (putative) occurrence, match
        score of the position, and the actual sequence including the ten
        positions before and after the motif occurrence (`site').
     
        Position-dependent Scoring Matrix
     
        The position-dependent scoring matrix corresponding to the motif is
        printed for use by database search programs such as MAST. This
        matrix is a log-odds matrix calculated by taking the log (base 2) of
        the ratio p/f at each position in the motif where p is the probability
        of a particular letter at that position in the motif, and f is the average
        frequency of that letter in the training set. The scoring matrix is
        printed "sideways"--columns correspond to the letters in the
        alphabet (in the same order as shown in the simplified motif) and
        rows corresponding to the positions of the motif, position one first.
        The scoring matrix is preceded by a line starting with "log-odds
        matrix:" and containing the length of the alphabet, width of the motif,
        number of characters in the training set and the scoring threshold
        used in the list of possible motif examples.
     
        Motif Letter-probability Matrix
     
        The motif itself is a position-dependent letter-probability matrix
        giving, for each position in the pattern, the probabilities of each
        possible letter occurring there. The letter-probability matrix is printed
        "sideways"--columns correspond to the letters in the alphabet (in
        the same order as shown in the simplified motif) and rows
        corresponding to the positions of the motif, position one first. The
        motif is preceded by a line starting with "letter-probability matrix:" and
        containing the length of the alphabet, width of the motif and number of
        characters in the training set.
    ********************************************************************************
    
    
    
    
    ********************************************************************************
    MOTIF  1		width =   9	sites = 29.5
    ********************************************************************************
    
    Simplified     A  ::1::::8:
    motif letter-  C  :::::::::
    probability    D  :8:::::::
    matrix         E  :::::::::
                   F  :::::::::
                   G  ::1:::::9
                   H  :::::::::
                   I  2:212::::
                   K  :::::::::
                   L  3:18:::::
                   M  :::::::::
                   N  :::::89::
                   P  :::::::::
                   Q  :::::::::
                   R  :::::::::
                   S  :::::::::
                   T  :::::::::
                   V  3:3:7::::
                   W  :::::::::
                   Y  :::::::::
    
    
             bits 6.7          
                  6.0          
                  5.4          
                  4.7          
    Information   4.0          
    content       3.4       *  
    (22.1 bits)   2.7  *   **  
                  2.0  * * ** *
                  1.3 ** ******
                  0.7 *********
                  0.0 ---------
    
    
    Multilevel        VDVLVNNAG
    consensus         L        
    sequence                   
                               
                               
    
    ----------------------------------------------------------------------
    	Possible examples of motif 1 in the training set
    ----------------------------------------------------------------------
    Sequence name             Start  Score              Site 
    -------------             -----  -----            ---------
    2BHD_STREX                   81  27.60 VAYAREEFGS VDGLVNNAG ISTGMFLETE
    3BHD_COMTE                   81  25.43 MAAVQRRLGT LNVLVNNAG ILLPGDMETG
    ADH_DROME                    86  20.80 LKTIFAQLKT VDVLINGAG ILDDHQIERT
    AP27_MOUSE                   77  23.29 TEKALGGIGP VDLLVNNAA LVIMQPFLEV
    BA72_EUBSP                   86  25.63 VGQVAQKYGR LDVMINNAG ITSNNVFSRV
    BDH_HUMAN                   138  22.74 PFEPEGPEKG MWGLVNNAG ISTFGEVEFT
    BPHB_PSEPS                   79  18.42 ASRCVARFGK IDTLIPNAG IWDYSTALVD
    BUDC_KLETE                   80  20.52 VEQARKALGG FNVIVNNAG IAPSTPIESI
    DHES_HUMAN                   84  24.73 AARERVTEGR VDVLVCNAG LGLLGPLEAL
    DHGB_BACME                   87  25.63 VQSAIKEFGK LDVMINNAG MENPVSSHEM
    DHMA_FLAS1                  198  15.82 ILVNMIAPGP VDVTGNNTG YSEPRLAEQV
    ENTA_ECOLI                   73  19.88 CQRLLAETER LDALVNAAG ILRMGATDQL
    FIXR_BRAJA                  112  22.78 EVKKRLAGAP LHALVNNAG VSPKTPTGDR
    GUTD_ECOLI                   82  16.09 SRGVDEIFGR VDLLVYSAG IAKAAFISDF
    HDE_CANTR                    92  20.26 VETAVKNFGT VHVIINNAG ILRDASMKKM
    HDE_CANTR                   396  28.82 IKNVIDKYGT IDILVNNAG ILRDRSFAKM
    HDHA_ECOLI                   89  29.35 ADFAISKLGK VDILVNNAG GGGPKPFDMP
    NODG_RHIME                   81  29.35 GQRAEADLEG VDILVNNAG ITKDGLFLHM
    RIDH_KLEAE                   89  15.33 LQGILQLTGR LDIFHANAG AYIGGPVAEG
    YINL_LISMO                   83  13.35 VELAIERYGK VDAIFLNAG IMPNSPLSAL
    YRTP_BACSU                   84  27.25 VAQVKEQLGD IDILINNAG ISKFGGFLDL
    CSGA_MYXXA                   13  28.10 AFATNVCTGP VDVLINNAG VSGLWCALGD
    DHB2_HUMAN                  161  18.93 KVAAMLQDRG LWAVINNAG VLGFPTDGEL
    DHB3_HUMAN                  125  17.96 HIKEKLAGLE IGILVNNVG MLPNLLPSHF
    DHCA_HUMAN                   83  29.40 RDFLRKEYGG LDVLVNNAG IAFKVADPTP
    FVT1_HUMAN                  115  23.34 IKQAQEKLGP VDMLVNCAG MAVSGKFEDL
    HMTR_LEIMA                  103  24.28 VAACYTHWGR CDVLVNNAS SFYPTPLLRN
    MAS1_AGRRA                  320  27.07 VTAAVEKFGR IDGLVNNAG YGEPVNLDKH
    PCR_PEA                     165  23.25 VDNFRRSEMP LDVLINNAA VYFPTAKEPS
    YURA_MYXXA                   90  16.83 IRALDAEAGG LDLVVANAG VGGTTNAKRL
    ----------------------------------------------------------------------
    
    
    log-odds matrix: alength= 20 w= 9 n= 9732 bayes= 8.36137
     -3.316   1.390  -5.130  -4.404   0.058  -4.789  -3.234   1.570  -4.081   1.829   0.447  -3.786  -2.854  -3.417  -4.034  -3.394  -2.682   2.096  -2.790  -2.790 
     -4.033  -3.269   4.095  -1.071  -4.174  -2.754  -0.610  -4.217  -3.875  -4.555  -4.136   0.118  -4.394  -3.117  -3.904  -3.169  -3.548  -4.336   0.889  -3.624 
      0.176  -1.770  -4.683  -4.057  -2.179   0.017  -2.875   1.767  -3.736   0.304   0.661  -2.809  -3.940  -3.061  -3.170  -3.013  -0.542   2.092  -2.559  -2.446 
     -3.975  -2.026  -4.994  -4.198  -0.445  -5.448  -3.389  -0.072  -3.964   3.061   0.853  -4.055  -3.998  -2.953  -3.660  -4.054  -1.412  -0.726  -2.922  -3.186 
     -1.964  -1.322  -3.749  -3.440  -0.950  -2.314  -0.190   1.486  -3.429  -2.219  -2.090  -3.363  -3.322  -3.106  -3.234  -2.706  -1.858   3.054  -3.177  -3.444 
     -2.471  -0.408  -2.158  -4.055  -3.667  -3.923  -0.612  -3.297  -3.104  -2.740  -3.592   4.531  -1.987  -2.320  -3.493  -1.798  -2.661  -4.113  -2.858  -1.451 
     -3.055  -0.342  -2.178  -4.043  -3.692  -2.752  -0.688  -3.329  -3.126  -4.240  -3.617   4.555  -3.737  -2.337  -3.524  -1.256  -2.532  -4.134  -2.882  -3.337 
      2.883  -0.565  -3.802  -3.403  -3.164  -2.439  -1.813  -2.816  -3.410  -3.111  -2.517  -3.254  -4.311  -3.103  -3.463  -0.982  -1.132  -1.123  -3.023  -3.059 
     -1.286  -3.261  -3.065  -3.746  -4.823   3.304  -3.368  -3.368  -3.582  -5.271  -4.466  -2.511  -4.230  -3.725  -3.621  -1.376  -4.067  -4.803  -3.714  -4.224 
    
    
    letter-probability matrix: alength= 20 w= 9 n= 9732
     0.011080  0.032025  0.001405  0.002686  0.038068  0.003217  0.001965  0.165994  0.003148  0.322410  0.037507  0.002644  0.005738  0.002833  0.003100  0.006207  0.008997  0.345601  0.001381  0.003994 
     0.006738  0.001268  0.841017  0.027062  0.002026  0.013179  0.012108  0.003008  0.003632  0.003860  0.001565  0.039559  0.001973  0.003488  0.003392  0.007253  0.004937  0.004001  0.017696  0.002240 
     0.124615  0.003583  0.001915  0.003418  0.008071  0.089970  0.002520  0.190285  0.004000  0.112016  0.043511  0.005203  0.002703  0.003624  0.005641  0.008084  0.039659  0.344488  0.001622  0.005070 
     0.007016  0.003000  0.001544  0.003098  0.026855  0.002037  0.001765  0.053208  0.003415  0.756863  0.049680  0.002194  0.002597  0.003906  0.004018  0.003928  0.021703  0.048874  0.001261  0.003037 
     0.028280  0.004887  0.003660  0.005242  0.018923  0.017877  0.016204  0.156612  0.004946  0.019488  0.006463  0.003543  0.004148  0.003514  0.005397  0.010000  0.015926  0.671296  0.001056  0.002539 
     0.019897  0.009211  0.011025  0.003422  0.002878  0.005864  0.012092  0.005691  0.006199  0.013578  0.002282  0.842847  0.010466  0.006059  0.004511  0.018761  0.009126  0.004671  0.001318  0.010104 
     0.013281  0.009641  0.010872  0.003450  0.002828  0.013202  0.011474  0.005567  0.006102  0.004802  0.002241  0.857100  0.003112  0.005987  0.004414  0.027305  0.009986  0.004603  0.001296  0.002735 
     0.813838  0.008258  0.003528  0.005378  0.004079  0.016395  0.005262  0.007941  0.005014  0.010497  0.004806  0.003820  0.002090  0.003520  0.004605  0.033031  0.026343  0.037103  0.001176  0.003315 
     0.045248  0.001275  0.005880  0.004238  0.001291  0.878111  0.001790  0.005418  0.004451  0.002350  0.001245  0.006394  0.002211  0.002287  0.004126  0.025136  0.003445  0.002896  0.000728  0.001478 
    
    
    
    
    Time 297.99 secs.
    
    
    
    ********************************************************************************
    MOTIF  2		width =  10	sites = 30.6
    ********************************************************************************
    Simplified     A  ::::531:::
    motif letter-  C  ::::1:::::
    probability    D  :::::1::::
    matrix         E  ::::::::::
                   F  ::::::::::
                   G  :::93219:9
                   H  ::::::::::
                   I  25::::::6:
                   K  ::::::2:::
                   L  51::::::2:
                   M  ::::::::::
                   N  :::::1::::
                   P  ::::::::::
                   Q  ::::::1:::
                   R  ::::::1:::
                   S  ::1:133:::
                   T  ::8:::::::
                   V  14::::::1:
                   W  ::::::::::
                   Y  ::::::::::
    
             bits 6.7           
                  6.0           
                  5.4           
                  4.7           
    Information   4.0           
    content       3.4           
    (23.0 bits)   2.7   **     *
                  2.0  ***   ***
                  1.3 *****  ***
                  0.7 **********
                  0.0 ----------
    
    Multilevel        LITGAASGIG
    consensus          V  GS    
    sequence               G    
                                
                                
    -----------------------------------------------------------------------
    	Possible examples of motif 2 in the training set
    -----------------------------------------------------------------------
    Sequence name             Start  Score               Site 
    -------------             -----  -----            ----------
    2BHD_STREX                   10  25.00  MNDLSGKTV IITGGARGLG AEAARQAVAA
    3BHD_COMTE                   10  24.81  TNRLQGKVA LVTGGASGVG LEVVKLLLGE
    AP27_MOUSE                   11  27.80 MKLNFSGLRA LVTGAGKGIG RDTVKALHAS
    BA72_EUBSP                   10  25.51  MNLVQDKVT IITGGTRGIG FAAAKIFIDN
    BDH_HUMAN                    59  23.13 AAEPVGSKAV LVTGCDSGFG FSLAKHLHSK
    BPHB_PSEPS                    9  26.22   MKLKGEAV LITGGASGLG RALVDRFVAE
    BUDC_KLETE                    6  27.30      MQKVA LVTGAGQGIG KAIALRLVKD
    DHES_HUMAN                    6  29.63      ARTVV LITGCSSGIG LHLAVRLASD
    DHGB_BACME                   11  20.81 MYKDLEGKVV VITGSSTGLG KSMAIRFATE
    DHII_HUMAN                   38  27.61 RPEMLQGKKV IVTGASKGIG REMAYHLAKM
    DHMA_FLAS1                   18  25.77 RPGRLAGKAA IVTGAAGGIG RATVEAYLRE
    ENTA_ECOLI                    9  26.79   MDFSGKNV WVTGAGKGIG YATALAFVEA
    FIXR_BRAJA                   40  25.09 RVDRGEPKVM LLTGASRGIG HATAKLFSEA
    GUTD_ECOLI                    6  12.85      MNQVA VVIGGGQTLG AFLCHGLAAE
    HDE_CANTR                    12  24.25 SPVDFKDKVV IITGAGGGLG KYYSLEFAKL
    HDE_CANTR                   326  23.93 PTVSLKDKVV LITGAGAGLG KEYAKWFAKY
    HDHA_ECOLI                   15  25.75 DNLRLDGKCA IITGAGAGIG KEIAITFATA
    LIGD_PSEPA                   10  20.38  MKDFQDQVA FITGGASGAG FGQAKVFGQA
    NODG_RHIME                   10  21.69  MFELTGRKA LVTGASGAIG GAIARVLHAQ
    RIDH_KLEAE                   18  24.83 MNTSLSGKVA AITGAASGIG LECARTLLGA
    YINL_LISMO                    9  28.91   MTIKNKVI IITGASSGIG KATALLLAEK
    YRTP_BACSU                   10  28.30  MQSLQHKTA LITGGGRGIG RATALALAKE
    DHB2_HUMAN                   86  23.63 ELLPVDQKAV LVTGGDCGLG HALCKYLDEL
    DHB3_HUMAN                   52  24.89 SFLRSMGQWA VITGAGDGIG KAYSFELAKR
    DHCA_HUMAN                    8  26.83    SSGIHVA LVTGGNKGIG LAIVRDLCRL
    FABI_ECOLI                   10  12.21  MGFLSGKRI LVTGVASKLS IAYGIAQAMH
    FVT1_HUMAN                   36  26.93 KPLALPGAHV VVTGGSSGIG KCIAIECYKQ
    HMTR_LEIMA                   10  20.41  MTAPTVPVA LVTGAAKRLG RSIAEGLHAE
    MAS1_AGRRA                  249  17.80 TVEIHQSPVI LVSGSNRGVG KAIAEDLIAH
    PCR_PEA                      90  25.41 GKKTLRKGNV VITGASSGLG LATAKALAES
    RFBB_NEIGO                   10  21.71  MQTEGKKNI LVTGGAGFIG SAVVRHIIQN
    YURA_MYXXA                  120   8.85 WERVRGIIDT NVTGAAATLS AVLPQMVERK
    -----------------------------------------------------------------------
    
    log-odds matrix: alength= 20 w= 10 n= 9699 bayes= 8.3045
     -1.611  -1.886  -4.941  -4.153  -0.143  -4.526  -2.998   1.807  -3.802   2.447  -1.369  -2.086  -3.972  -3.029  -3.680  -3.212  -2.527   0.761   1.445  -2.399 
     -3.505  -1.107  -4.745  -4.400  -1.129  -4.838  -3.491   3.049  -4.044  -0.826  -1.706  -3.873  -4.360  -3.611  -3.453  -3.548  -2.738   2.317  -3.208  -3.054 
     -3.822  -2.373  -4.182  -4.547  -4.279  -5.128  -3.594  -1.270  -3.681  -4.502  -3.152  -2.508  -4.228  -3.067  -3.800  -0.110   3.945  -2.130  -3.929  -4.486 
     -2.480  -3.319  -2.766  -3.763  -4.815   3.498  -3.361  -4.939  -3.574  -4.785  -4.505  -2.686  -4.258  -3.716  -3.614  -2.887  -4.016  -4.854  -3.742  -4.290 
      2.156   2.239  -5.339  -5.005  -4.638   1.948  -4.590  -4.417  -4.995  -3.814  -4.017  -4.564  -4.724  -3.653  -4.877   0.121  -3.114  -1.547  -4.569  -4.936 
      1.327  -3.608   0.426  -2.949  -5.103   1.536  -2.684  -5.215  -2.992  -2.392  -4.701   0.780  -4.205  -2.631  -3.616   1.991  -0.622  -4.806  -4.926  -4.264 
     -0.600   1.151  -0.420  -1.334  -3.513   0.359  -1.425  -3.224   1.535  -3.390  -2.760  -1.653  -2.913   1.038   1.521   2.105  -0.457  -3.450  -3.256  -2.751 
     -1.991  -3.324  -3.141  -3.762  -1.103   3.391  -3.393  -4.915  -1.671  -5.400  -4.486  -2.576  -4.256  -3.728  -1.326  -2.888  -1.487  -4.811  -3.736  -4.244 
     -2.220  -2.663  -4.568  -4.441  -0.717  -5.093  -3.990   3.488  -4.017   1.029  -1.412  -3.987  -4.632  -3.765  -4.347  -3.770  -2.976   0.354  -3.430  -3.191 
     -3.185  -3.326  -3.109  -3.768  -4.822   3.483  -3.397  -4.905  -3.244  -5.360  -4.506  -2.671  -4.256  -3.687  -3.603  -1.246  -3.807  -4.824  -3.742  -4.290 
    
    letter-probability matrix: alength= 20 w= 10 n= 9699
     0.036508  0.003317  0.001677  0.003211  0.033203  0.003538  0.002352  0.190393  0.003792  0.502095  0.010864  0.009793  0.002663  0.003700  0.003929  0.006850  0.009557  0.140870  0.026408  0.005279 
     0.009821  0.005693  0.001921  0.002706  0.016762  0.002851  0.001672  0.450462  0.003207  0.051966  0.008600  0.002837  0.002035  0.002471  0.004599  0.005424  0.008258  0.414313  0.001049  0.003354 
     0.007884  0.002367  0.002837  0.002443  0.001888  0.002331  0.001556  0.022576  0.004124  0.004066  0.003158  0.007310  0.002229  0.003603  0.003615  0.058806  0.848339  0.018990  0.000637  0.001243 
     0.019983  0.001228  0.007567  0.004207  0.001302  0.921021  0.001829  0.001774  0.004444  0.003341  0.001236  0.006461  0.002184  0.002298  0.004114  0.008581  0.003404  0.002875  0.000725  0.001424 
     0.497179  0.057863  0.001272  0.001778  0.001472  0.314556  0.000780  0.002548  0.001659  0.006549  0.001733  0.001758  0.001581  0.002400  0.001714  0.069019  0.006364  0.028459  0.000408  0.000910 
     0.279861  0.001006  0.069195  0.007395  0.001067  0.236434  0.002925  0.001466  0.006649  0.017550  0.001079  0.071398  0.002266  0.004876  0.004109  0.252178  0.035807  0.002972  0.000319  0.001450 
     0.073567  0.027220  0.038496  0.022646  0.003213  0.104546  0.006996  0.005825  0.153324  0.008786  0.004142  0.013216  0.005548  0.062001  0.144517  0.273064  0.040131  0.007610  0.001015  0.004136 
     0.028048  0.001224  0.005838  0.004209  0.017069  0.855067  0.001789  0.001804  0.016618  0.002181  0.001252  0.006970  0.002187  0.002279  0.020085  0.008570  0.019647  0.002963  0.000728  0.001470 
     0.023937  0.001935  0.002171  0.002629  0.022304  0.002388  0.001182  0.610812  0.003267  0.187978  0.010548  0.002621  0.001685  0.002221  0.002475  0.004650  0.007004  0.106243  0.000899  0.003049 
     0.012264  0.001223  0.005967  0.004192  0.001297  0.911416  0.001784  0.001816  0.005584  0.002242  0.001235  0.006526  0.002187  0.002344  0.004144  0.026762  0.003935  0.002935  0.000725  0.001424 
    
    
    
    
    Time 602.81 secs.
    
    
    
    ********************************************************************************
    MOTIF  3		width =  13	sites = 31.4
    ********************************************************************************
    Simplified     A  :171:47111:1:
    motif letter-  C  :::::::::::::
    probability    D  ::::::::1::::
    matrix         E  ::::::::1:::2
                   F  :::::2::::2::
                   G  :1:::12::3:::
                   H  :::::::::1::1
                   I  :::::::11::::
                   K  ::::9:::1:::2
                   L  :::::::21:7::
                   M  :::::::1:1:1:
                   N  :::::::::1:::
                   P  :::::::::::::
                   Q  ::::::::::::1
                   R  ::::::::1:::2
                   S  :517::::11:21
                   T  :1:2::::1::4:
                   V  :::::::41::1:
                   W  :::::1:::::::
                   Y  a::::::::::::
    
             bits 6.7              
                  6.0              
                  5.4              
                  4.7 *            
    Information   4.0 *            
    content       3.4 *   *        
    (26.7 bits)   2.7 *   *        
                  2.0 *  **     *  
                  1.3 ***** *   ** 
                  0.7 ******** ****
                  0.0 -------------
    
    Multilevel        YSASKAAVxGLTR
    consensus              F L    E
    sequence                       
                                   
                                   
    --------------------------------------------------------------------------
    	Possible examples of motif 3 in the training set
    --------------------------------------------------------------------------
    Sequence name             Start  Score                Site   
    -------------             -----  -----            -------------
    2BHD_STREX                  152  30.78 GLMGLALTSS YGASKWGVRGLSK LAAVELGTDR
    3BHD_COMTE                  151  34.37 SWLPIEQYAG YSASKAAVSALTR AAALSCRKQG
    ADH_DROME                   152  25.46 GFNAIYQVPV YSGTKAAVVNFTS SLAKLAPITG
    AP27_MOUSE                  149  29.96 AHVTFPNLIT YSSTKGAMTMLTK AMAMELGPHK
    BA72_EUBSP                  157  28.01 GIFGSLSGVG YPASKASVIGLTH GLGREIIRKN
    BDH_HUMAN                   208  21.60 GRMANPARSP YCITKFGVEAFSD CLRYEMYPLG
    BPHB_PSEPS                  153  24.39 GFYPNGGGPL YTAAKQAIVGLVR ELAFELAPYV
    BUDC_KLETE                  152  34.42 GHVGNPELAV YSSSKFAVRGLTQ TAARDLAPLG
    DHES_HUMAN                  155  32.89 GLMGLPFNDV YCASKFALEGLCE SLAVLLLPFG
    DHGB_BACME                  160  22.13 WKIPWPLFVH YAASKGGMKLMTE TLALEYAPKG
    DHII_HUMAN                  183  29.96 GKVAYPMVAA YSASKFALDGFFS SIRKEYSVSR
    DHMA_FLAS1                  165  23.00 SFMAEPEAAA YVAAKGGVAMLTR AMAVDLARHG
    ENTA_ECOLI                  144  22.81 AHTPRIGMSA YGASKAALKSLAL SVGLELAGSG
    FIXR_BRAJA                  189  24.64 SRVHPFAGSA YATSKAALASLTR ELAHDYAPHG
    GUTD_ECOLI                  154  26.21 GKVGSKHNSG YSAAKFGGVGLTQ SLALDLAEYG
    HDE_CANTR                   163  15.37 GLYGNFGQAN YASAKSALLGFAE TLAKEGAKYN
    HDE_CANTR                   467  28.38 GIYGNFGQAN YSSSKAGILGLSK TMAIEGAKNN
    HDHA_ECOLI                  159  25.05 AENKNINMTS YASSKAAASHLVR NMAFDLGEKN
    LIGD_PSEPA                  157  26.29 GFMGSALAGP YSAAKAASINLME GYRQGLEKYG
    NODG_RHIME                  152  30.31 GAIGNPGQTN YCASKAGMIGFSK SLAQEIATRN
    RIDH_KLEAE                  160  29.06 GVVPVIWEPV YTASKFAVQAFVH TTRRQVAQYG
    YINL_LISMO                  154  27.95 GLKAYPGGAV YGATKWAVRDLME VLRMESAQEG
    YRTP_BACSU                  155  35.05 GQRGAAVTSA YSASKFAVLGLTE SLMQEVRKHN
    CSGA_MYXXA                   88  21.27 AANTDGGAYA YRMSKAALNMAVR SMSTDLRPEG
    DHB2_HUMAN                  232  27.37 GGAPMERLAS YGSSKAAVTMFSS VMRLELSKWG
    DHB3_HUMAN                  198  30.12 ALFPWPLYSM YSASKAFVCAFSK ALQEEYKAKE
    DHCA_HUMAN                  193  18.86 HQKEGWPSSA YGVTKIGVTVLSR IHARKLSEQR
    FVT1_HUMAN                  186  31.79 GQLGLFGFTA YSASKFAIRGLAE ALQMEVKPYN
    HMTR_LEIMA                  193  26.46 TNQPLLGYTI YTMAKGALEGLTR SAALELAPLQ
    MAS1_AGRRA                  392  24.07 GQRVLNPLVG YNMTKHALGGLTK TTQHVGWDRR
    RFBB_NEIGO                  165  30.45 ETTPYAPSSP YSASKAAADHLVR AWQRTYRLPS
    YURA_MYXXA                  160  28.06 AGFRGLPATR YSASKAFLSTFME SLRVDLRGTG
    --------------------------------------------------------------------------
    
    log-odds matrix: alength= 20 w= 13 n= 9600 bayes= 8.25243
     -6.789  -4.769  -6.508  -6.871  -1.048  -6.141  -2.789  -5.559  -5.658  -4.975  -2.791  -4.011  -5.723  -5.118  -5.602  -5.574  -6.098  -5.094  -1.942   5.260 
     -0.748   2.026  -3.223  -3.163  -3.486  -0.087  -2.670  -3.739  -2.445  -3.541  -3.104  -0.597  -1.084  -2.467  -1.155   3.159   1.047  -2.002  -3.371  -3.079 
      2.645  -0.605  -3.718  -3.429  -3.071  -1.575  -3.240  -1.481  -3.343  -2.871   0.836  -3.491  -4.376  -3.134  -3.475   0.780  -1.130  -1.217  -3.066  -3.394 
     -0.082  -1.742  -3.838  -4.239  -3.822  -4.021  -3.032  -4.216  -3.327  -4.352  -3.327  -2.166  -3.530  -3.299  -3.374   3.462   1.561  -4.535  -3.683  -3.496 
     -4.089  -2.986  -4.803  -4.292  -5.176  -5.166  -3.412  -4.097   4.201  -4.875  -4.126  -3.484  -4.344  -3.485  -0.518  -4.217  -3.880  -5.087  -3.716  -4.383 
      1.914  -1.807  -4.291  -3.382   2.600   0.280   0.639  -0.404  -3.076  -1.953  -1.729  -3.400  -3.949   0.010  -3.435  -2.381  -2.372  -1.848   2.470  -2.426 
      2.607  -0.890  -4.642  -4.202   0.420   1.041  -3.921  -3.853  -4.066  -3.604  -3.313  -4.060  -4.580  -3.799  -3.828  -0.432  -2.808  -2.726  -3.831  -4.171 
     -0.691  -1.285  -4.853  -3.634  -2.198  -1.560  -2.965   0.804  -3.704   1.394   1.746  -3.327  -4.045  -3.171  -3.412  -0.806  -2.387   2.164  -2.633  -2.403 
     -0.647   1.131   0.279   0.836  -3.468  -1.444  -1.452   0.471   0.588  -0.639  -2.431  -0.072  -2.918   0.459   1.217   0.649   0.682  -0.016  -3.267  -2.524 
      0.150  -2.907  -0.431  -1.415  -3.268   1.924   1.623  -3.152  -1.238  -1.342   1.991   0.579  -2.880  -0.921  -1.913   0.175  -0.534  -1.280  -2.888  -2.522 
     -2.195  -2.777  -5.264  -4.382   2.102  -5.476  -3.547  -1.579  -4.054   2.961   0.295  -3.691  -4.207  -3.149  -3.841  -3.993  -3.336  -2.482  -3.064  -3.127 
     -0.877   1.153  -4.536  -4.150  -0.301  -4.908  -3.270  -2.261  -3.092  -2.847   1.559  -2.734  -4.212  -3.125  -3.269   1.663   2.879   0.716  -2.943  -3.168 
     -2.700  -3.239  -0.524   1.824  -3.629  -3.654   1.643  -3.709   1.851  -1.438  -2.841  -1.720  -2.836   1.202   2.315   0.628  -2.150  -3.612  -3.359  -2.740 
    
    letter-probability matrix: alength= 20 w= 13 n= 9600
     0.000978  0.000447  0.000570  0.000484  0.017138  0.001278  0.002673  0.001233  0.000989  0.002934  0.003884  0.002593  0.000797  0.000872  0.001030  0.001274  0.000821  0.002459  0.002522  0.955023 
     0.064402  0.049632  0.005562  0.006325  0.003162  0.084904  0.002903  0.004357  0.009175  0.007928  0.003124  0.027640  0.019870  0.005475  0.022471  0.542024  0.116183  0.020975  0.000937  0.002950 
     0.676781  0.008011  0.003947  0.005260  0.004217  0.030271  0.001955  0.020837  0.004924  0.012609  0.047975  0.003718  0.002028  0.003447  0.004500  0.104184  0.025680  0.036128  0.001158  0.002370 
     0.102160  0.003643  0.003632  0.002999  0.002505  0.005555  0.002259  0.003131  0.004979  0.004517  0.002677  0.009312  0.003645  0.003076  0.004826  0.668679  0.165818  0.003623  0.000755  0.002209 
     0.006355  0.001538  0.001860  0.002893  0.000980  0.002512  0.001735  0.003400  0.919107  0.003144  0.001539  0.003735  0.002073  0.002703  0.034940  0.003263  0.003819  0.002471  0.000738  0.001195 
     0.407591  0.003483  0.002654  0.005432  0.214825  0.109438  0.028769  0.043959  0.005925  0.023826  0.008104  0.003960  0.002727  0.030487  0.004627  0.011645  0.010860  0.023340  0.053711  0.004638 
     0.659085  0.006577  0.002080  0.003078  0.047386  0.185556  0.001219  0.004026  0.002983  0.007590  0.002703  0.002505  0.001761  0.002175  0.003524  0.044960  0.008028  0.012700  0.000681  0.001383 
     0.067010  0.005001  0.001797  0.004563  0.007719  0.030571  0.002366  0.101552  0.003834  0.242438  0.090110  0.004165  0.002550  0.003361  0.004702  0.034702  0.010745  0.376540  0.001563  0.004713 
     0.069057  0.026677  0.063036  0.101116  0.003202  0.033133  0.006750  0.080639  0.075134  0.059240  0.004982  0.039782  0.005573  0.041613  0.116364  0.095109  0.090162  0.083094  0.001007  0.004334 
     0.119989  0.001625  0.038517  0.021240  0.003677  0.342149  0.056885  0.006543  0.021186  0.036405  0.106786  0.062460  0.005722  0.015988  0.013286  0.068492  0.038813  0.034588  0.001309  0.004339 
     0.023627  0.001778  0.001351  0.002717  0.152150  0.002025  0.001580  0.019466  0.003009  0.718492  0.032960  0.003237  0.002281  0.003412  0.003492  0.003810  0.005567  0.015033  0.001159  0.002853 
     0.058901  0.027091  0.002238  0.003192  0.028758  0.003003  0.001915  0.012137  0.005861  0.012824  0.079192  0.006284  0.002272  0.003471  0.005191  0.192171  0.413450  0.138016  0.001261  0.002773 
     0.016647  0.001291  0.036131  0.200603  0.002863  0.007161  0.057665  0.004447  0.180282  0.034047  0.003750  0.012691  0.005899  0.069646  0.248936  0.093732  0.012665  0.006871  0.000945  0.003730 
    
    
    
    
    Time 862.02 secs.
    
    Stopped because nmotifs = 3 reached.
    
    CPU: paragon
    
    
    
    
    ********************************************************************************
    DEBUG INFORMATION
    ********************************************************************************
    Some of the information in this section is used by MAST.
    Please do not delete it if you wish to search sequence databases for
    matches to the above motifs.  This information can also be useful in the
    event you wish to report a problem with the MEME software.
    
    ALPHABET= ACDEFGHIKLMNPQRSTVWY
    DATAFILE= meme.7209850.data (deleted by web version of MEME)
    model:  mod=         zoops    nmotifs=         3    chi=             1
    width:  minw=           12    maxw=           55    shorten=       yes
    lambda: minsites=        0    maxsites=       33
    theta:  prob=            1    spmap=         pam    spfuzz=        120
    em:     prior=       megap    b=           99960    maxiter=        20
            distance=    0.001
    data:   n=            9996    N=              33
    strands:    w53
    sample: seed=            0    seqfrac=         1
    LRT:    adj=          root
    Dirichlet mixture priors file: prior30.plib
    Letter frequencies:
    A 0.111 C 0.012 D 0.050 E 0.055 F 0.036 G 0.090 H 0.018 I 0.057 K 0.052
    L 0.092 M 0.027 N 0.041 P 0.041 Q 0.029 R 0.049 S 0.064 T 0.057 V 0.083
    W 0.010 Y 0.027
    Effective length of alphabet = 20
    Entropy of dataset (bits) =    -4.11
    
    /mount4a/app/tbailey/meme.1.95/bin/intelparagon_p/meme meme.7209850.data -protein -mod zoops -nmotifs 3 -maxw 55 -minw 12 -nostatus -maxiter 20 -maxsize 10000 
    ********************************************************************************