annotate test-data/meme_output_test2.txt @ 4:e24560178fad draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 8c1eac566cbcc93ceb3d753170bce144d386722c"

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MEME - Motif discovery tool
MEME version 5.0.5 (Release date: Mon Mar 18 20:12:19 2019 -0700)
REFERENCE
TRAINING SET
PRIMARY SEQUENCES= Galaxy_FASTA_Input
CONTROL SEQUENCES= --none--
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
chr21_19617074_19617124_ 1.0000     50  chr21_26934381_26934431_ 1.0000     50  
COMMAND LINE SUMMARY
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=       30    wnsites=       0.8
theta:  spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    0.001
trim:   wg=             11    ws=              1    endgaps=       yes
data:   n=            1500    N=              30
sample: seed=            0    hsfrac=          0
        searchsize=   1500    norand=         no    csites=       1000
Dirichlet mixture priors file:
Letter frequencies in dataset:
A 0.294 C 0.231 G 0.257 T 0.217 
Background letter frequencies (from file dataset with add-one prior applied):
A 0.294 C 0.231 G 0.257 T 0.217 
Background model order: 0
MOTIF GGSRTATAAAA MEME-1	width =  11  sites =  30  llr = 254  E-value = 5.1e-040
	Motif GGSRTATAAAA MEME-1 Description
Simplified        A  3313:9:a798
pos.-specific     C  1:3::1:::1:
probability       G  6756::::::2
matrix            T  1:11a1a:3::

         bits    2.2       *    
                 2.0     * *    
                 1.8     * *    
                 1.5     * ** * 
Relative         1.3     * ** * 
Entropy          1.1     ****** 
(12.2 bits)      0.9  *  *******
                 0.7  *  *******
                 0.4 ** ********
                 0.2 ***********
                 0.0 -----------

Multilevel           GGGGTATAAAA
consensus            AACA    T  
sequence                        
	Motif GGSRTATAAAA MEME-1 sites sorted by position p-value
Sequence name             Start   P-value               Site  
chr21_46046964_46047014_     13  4.51e-07 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC
	Motif GGSRTATAAAA MEME-1 block diagrams
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
chr21_46046964_46047014_          4.5e-07  12_[+1]_27
	Motif GGSRTATAAAA MEME-1 in BLOCKS format
BL   MOTIF GGSRTATAAAA width=11 seqs=30
chr21_46046964_46047014_ (   13) GGGGTATAAAA  1 
	Motif GGSRTATAAAA MEME-1 position-specific scoring matrix
log-odds matrix: alength= 4 w= 11 n= 1200 bayes= 5.2854 E= 5.1e-040 
   -14   -179    114   -112 
     3  -1155    137   -270 
  -114     20     86    -71 
     3   -279    122   -170 
 -1155  -1155   -295    215 
   156   -179  -1155   -170 
 -1155  -1155  -1155    220 
   172   -279  -1155  -1155 
   125  -1155  -1155     46 
   167   -179  -1155  -1155 
   144  -1155    -63   -270 
	Motif GGSRTATAAAA MEME-1 position-specific probability matrix
letter-probability matrix: alength= 4 w= 11 nsites= 30 E= 5.1e-040 
 0.266667  0.066667  0.566667  0.100000 
	Motif GGSRTATAAAA MEME-1 regular expression
[GA][GA][GC][GA]TATA[AT]AA
SUMMARY OF MOTIFS
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
chr21_19617074_19617124_         5.63e-04  39_[+1(1.41e-05)]
Stopped because requested number of motifs (1) found.