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MEME - Motif discovery tool
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MEME version 4.12.0 (Release date: Thu Jul 27 17:36:34 2017 -0700)

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme-suite.org .

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-suite.org .
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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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PRIMARY SEQUENCES= ../common/lex0.s
CONTROL SEQUENCES= --none--
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
cloacin-df13             1.0000    200  colicin-e1               1.0000    200  
colicin-ia               1.0000    200  colicin-ib               1.0000    200  
reca                     1.0000    200  recn                     1.0000    200  
sula                     1.0000    200  umu-operon               1.0000    200  
uvra                     1.0000    200  uvrb                     1.0000    200  
uvrd                     1.0000    200  colicin-a                1.0000    136  
lexA                     1.0000    173  muc-operon               1.0000    158  
hima                     1.0000    200  uvrc                     1.0000    200  
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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 -dna -pal ../common/lex0.s -text 

model:  mod=         zoops    nmotifs=         1    evt=           inf
objective function:           em=       E-value of product of p-values
                              starts=   E-value of product of p-values
strands: +
width:  minw=            8    maxw=           50
nsites: minsites=        2    maxsites=       16    wnsites=       0.8
theta:  spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
trim:   wg=             11    ws=              1    endgaps=       yes
data:   n=            3067    N=              16
sample: seed=            0    hsfrac=          0    maxwords=       -1
        maxsize=    100000    csites=       1000
Letter frequencies in dataset:
A 0.296 C 0.207 G 0.213 T 0.283 
Background letter frequencies (from file dataset with add-one prior applied):
A 0.296 C 0.207 G 0.213 T 0.283 
Background model order: 0
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MOTIF WACTGTATATATATACAGTW MEME-1	width =  20  sites =  14  llr = 216  E-value = 1.9e-024
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	Motif WACTGTATATATATACAGTW MEME-1 Description
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Simplified        A  471:::7:6172a27:a:16
pos.-specific     C  119::::::1:2:12a::1:
probability       G  :1::a31:2:1::::::911
matrix            T  61:a:72a2716:7:::174

         bits    2.3     *          *    
                 2.0     *          *    
                 1.8   ***          **   
                 1.6   ***  *    *  ***  
Relative         1.4   ***  *    *  ***  
Entropy          1.1   ***  *    *  ***  
(22.2 bits)      0.9   **** *    * ****  
                 0.7   ****** ********** 
                 0.5 ********************
                 0.2 ********************
                 0.0 --------------------

Multilevel           TACTGTATATATATACAGTA
consensus            A    G        C    T
sequence                                 
                                         
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	Motif WACTGTATATATATACAGTW MEME-1 sites sorted by position p-value
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Sequence name             Start   P-value                    Site      
-------------             ----- ---------            --------------------
cloacin-df13                 97  5.39e-11 gtaataatca tactgtgtatatatacagta ttttggtttt
umu-operon                   91  7.82e-10 aagaacagac tactgtatataaaaacagta taacttcagg
muc-operon                   49  2.55e-09 ataacagcga tactgtataaataaacagtt atttggaaga
recn                         71  4.07e-09 ccagcctctt tactgtatataaaaccagtt tatactgtac
reca                         71  1.95e-08 aaacacttga tactgtatgagcatacagta taattgcttc
uvrb                         71  2.36e-08 tatggtgatg aactgtttttttatccagta taatttgttg
sula                         85  7.93e-08 tcactggatg tactgtacatccatacagta actcacaggg
uvrd                        102  9.28e-08 taatcagcaa atctgtatatatacccagct ttttggcgga
lexA                         76  1.00e-07 ctcacagcat aactgtatatacacccaggg ggcggaatga
colicin-a                    34  1.17e-07 agtatcattt tactgtatataaacacatgt gaatatatac
colicin-ib                   99  1.17e-07 aataaattag tactgtatatgtatccatat acgtaagcag
colicin-ia                   99  1.17e-07 aataaattaa tactgtatatgtatccatat gcgtaagcag
colicin-e1                   97  1.26e-07 gtagctttta tgctgtatataaaaccagtg gttatatgta
uvra                         60  1.82e-07 tgcattccaa tactgtatattcattcaggt caatttgtgt
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	Motif WACTGTATATATATACAGTW MEME-1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
cloacin-df13                      5.4e-11  96_[+1]_84
umu-operon                        7.8e-10  90_[+1]_90
muc-operon                        2.6e-09  48_[+1]_90
recn                              4.1e-09  70_[+1]_110
reca                              1.9e-08  70_[+1]_110
uvrb                              2.4e-08  70_[+1]_110
sula                              7.9e-08  84_[+1]_96
uvrd                              9.3e-08  101_[+1]_79
lexA                                1e-07  75_[+1]_78
colicin-a                         1.2e-07  33_[+1]_83
colicin-ib                        1.2e-07  98_[+1]_82
colicin-ia                        1.2e-07  98_[+1]_82
colicin-e1                        1.3e-07  96_[+1]_84
uvra                              1.8e-07  59_[+1]_121
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	Motif WACTGTATATATATACAGTW MEME-1 in BLOCKS format
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BL   MOTIF WACTGTATATATATACAGTW width=20 seqs=14
cloacin-df13             (   97) TACTGTGTATATATACAGTA  1 
umu-operon               (   91) TACTGTATATAAAAACAGTA  1 
muc-operon               (   49) TACTGTATAAATAAACAGTT  1 
recn                     (   71) TACTGTATATAAAACCAGTT  1 
reca                     (   71) TACTGTATGAGCATACAGTA  1 
uvrb                     (   71) AACTGTTTTTTTATCCAGTA  1 
sula                     (   85) TACTGTACATCCATACAGTA  1 
uvrd                     (  102) ATCTGTATATATACCCAGCT  1 
lexA                     (   76) AACTGTATATACACCCAGGG  1 
colicin-a                (   34) TACTGTATATAAACACATGT  1 
colicin-ib               (   99) TACTGTATATGTATCCATAT  1 
colicin-ia               (   99) TACTGTATATGTATCCATAT  1 
colicin-e1               (   97) TGCTGTATATAAAACCAGTG  1 
uvra                     (   60) TACTGTATATTCATTCAGGT  1 
//

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	Motif WACTGTATATATATACAGTW MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 20 n= 2763 bayes= 8.84392 E= 1.9e-024 
    27   -154  -1047    101 
   127    -95   -157   -140 
  -147    211  -1047  -1042 
 -1048  -1043  -1047    182 
 -1048  -1043    223  -1042 
  -305  -1043     23    133 
   119  -1043    -58    -67 
 -1048   -253  -1047    177 
   112  -1043    -25    -67 
  -105    -95   -257    133 
   127   -253    -99    -99 
   -73    -22  -1048    118 
   170  -1044   -257  -1043 
   -73    -54  -1048    126 
   127     27  -1048   -298 
 -1049    227  -1048  -1043 
   175  -1044  -1048  -1043 
 -1049  -1044    207   -140 
  -147   -154    -99    133 
    95  -1044   -157     33 
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	Motif WACTGTATATATATACAGTW MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 20 nsites= 14 E= 1.9e-024 
 0.357143  0.071429  0.000000  0.571429 
 0.714286  0.107143  0.071429  0.107143 
 0.107143  0.892857  0.000000  0.000000 
 0.000000  0.000000  0.000000  1.000000 
 0.000000  0.000000  1.000000  0.000000 
 0.035714  0.000000  0.250000  0.714286 
 0.678571  0.000000  0.142857  0.178571 
 0.000000  0.035714  0.000000  0.964286 
 0.642857  0.000000  0.178571  0.178571 
 0.142856  0.107141  0.035713  0.714284 
 0.714285  0.035714  0.107142  0.142857 
 0.178570  0.178570  0.000000  0.642856 
 0.964285  0.000000  0.035713  0.000000 
 0.178570  0.142856  0.000000  0.678570 
 0.714285  0.249999  0.000000  0.035713 
 0.000000  0.999999  0.000000  0.000000 
 0.999999  0.000000  0.000000  0.000000 
 0.000000  0.000000  0.892856  0.107142 
 0.107142  0.071428  0.107142  0.714285 
 0.571428  0.000000  0.071428  0.357142 
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	Motif WACTGTATATATATACAGTW MEME-1 regular expression
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[TA]ACTG[TG]ATATATAT[AC]CAGT[AT]
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Time  1.00 secs.

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SUMMARY OF MOTIFS
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	Combined block diagrams: non-overlapping sites with p-value < 0.0001
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SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
cloacin-df13                     9.75e-09  96_[+1(5.39e-11)]_84
colicin-e1                       2.28e-05  96_[+1(1.26e-07)]_84
colicin-ia                       2.11e-05  98_[+1(1.17e-07)]_82
colicin-ib                       2.11e-05  98_[+1(1.17e-07)]_82
reca                             3.53e-06  70_[+1(1.95e-08)]_110
recn                             7.36e-07  70_[+1(4.07e-09)]_20_[+1(1.02e-06)]_\
    70
sula                             1.44e-05  84_[+1(7.93e-08)]_96
umu-operon                       1.42e-07  90_[+1(7.82e-10)]_90
uvra                             3.29e-05  59_[+1(1.82e-07)]_121
uvrb                             4.27e-06  70_[+1(2.36e-08)]_110
uvrd                             1.68e-05  101_[+1(9.28e-08)]_79
colicin-a                        1.37e-05  33_[+1(1.17e-07)]_83
lexA                             1.54e-05  54_[+1(9.22e-06)]_1_[+1(1.00e-07)]_\
    78
muc-operon                       3.55e-07  48_[+1(2.55e-09)]_90
hima                             9.65e-01  200
uvrc                             9.02e-01  200
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Stopped because requested number of motifs (1) found.
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CPU: Timothys-iMac.rd.unr.edu

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