FIMO Results

FIMO - Motif search tool

FIMO version 4.3.0, (Release date: 6 PDT 20)

For further information on how to interpret these results or to get a copy of the FIMO software please access http://meme.nbcr.net

DATABASE AND MOTIFS

        DATABASE 
        pr6.fasta

        Database contains 
        1
        sequences,
        29926
        residues
      

        MOTIFS 
        meme.txt 
        (nucleotide)
        


MOTIF
WIDTH

              BEST POSSIBLE MATCH
            


1
37
GTTTGGAAACTCTTGTTAGATCTCATTAAATCTAAAC

2
29
GGTAACTATCGTTTACCGTCTAGTAAACC

3
7
CCACCCA


        Random model letter frequencies 
        (from non-redundant database):
        
A 0.282 C 0.222 G 0.229 T 0.267 

MOTIF	WIDTH	BEST POSSIBLE MATCH
1	37	GTTTGGAAACTCTTGTTAGATCTCATTAAATCTAAAC
2	29	GGTAACTATCGTTTACCGTCTAGTAAACC
3	7	CCACCCA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

Each of the following 15 motif occurrences has p-value less then 0.0001
The p-value of a motif occurrence is defined as the probability of a random sequence of the same length as the motif matching that position of the sequence with as good or better a score.
The score for the match of a position in a sequence to a motif is computed by by summing the appropriate entries from each column of the position-dependent scoring matrix that represents the motif.
The q-value of a motif occurrence is defined as the false discovery rate if the occurrence is accepted as significant.
The table is sorted by increasing p-value.
If the start position is larger then the end position, the motif occurrence is on the reverse strand.

Motif	Sequence Name	Start	End	p-value	q-value
1	NC_006577.2	27007	27043	1.47e-18	1.04e-14
1	NC_006577.2	35	71	2.32e-17	8.18e-14
1	NC_006577.2	21735	21771	3.52e-16	8.26e-13
1	NC_006577.2	28276	28312	4.79e-15	8.44e-12
1	NC_006577.2	22905	22941	2.91e-14	4.1e-11
1	NC_006577.2	4430	4466	2.24e-06	0.00263
1	NC_006577.2	20715	20751	1.68e-05	0.017
1	NC_006577.2	23446	23482	2.85e-05	0.0251
1	NC_006577.2	25154	25190	3.8e-05	0.0298
1	NC_006577.2	22316	22352	4.5e-05	0.0317
1	NC_006577.2	26365	26401	7e-05	0.0436
1	NC_006577.2	18931	18967	8.13e-05	0.0436
1	NC_006577.2	29760	29796	8.54e-05	0.0436
1	NC_006577.2	29626	29662	8.69e-05	0.0436
1	NC_006577.2	25756	25792	9.27e-05	0.0436

DEBUGGING INFORMATION

Command line:

fimo --o pr6_origres --motif 1 --norc meme.txt pr6.fasta

Settings:



output directory = pr6_origres
MEME file name = meme.txt
sequence file name = pr6.fasta


background file name = (null)
motif name = motif
allow clobber = false


compute q-values = true
output p-threshold set = false
output q-threshold set = false


text only = false
scan both strands = false
max sequence length = 250000000


output q-value threshold =   1
output p-value threshold = 0.0001
pseudocount = 0.1


verbosity = 2
selected motif = 1
 =

This information can be useful in the event you wish to report a problem with the FIMO software.

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output directory = pr6_origres	MEME file name = meme.txt	sequence file name = pr6.fasta
background file name = (null)	motif name = motif	allow clobber = false
compute q-values = true	output p-threshold set = false	output q-threshold set = false
text only = false	scan both strands = false	max sequence length = 250000000
output q-value threshold = 1	output p-value threshold = 0.0001	pseudocount = 0.1
verbosity = 2	selected motif = 1	=