FIMO Results

FIMO - Motif search tool

FIMO version 4.10.0, (Release date: Wed May 21 10:35:36 2014 +1000)

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

If you use FIMO in your research, please cite the following paper:
Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, "FIMO: Scanning for occurrences of a given motif", Bioinformatics, 27(7):1017-1018, 2011. [full text]

DATABASE AND MOTIFS

        DATABASE 
        Static_Male-biased_Output/Static_Male-biased.fa

        Database contains 
        1954
        sequences,
        977000
        residues
      

        MOTIFS 
        Static_Male-biased_Output/dreme_out/dreme.xml 
        (nucleotide)
        


MOTIF
WIDTH

              BEST POSSIBLE MATCH
            


ATYGATY
7
ATTGATT

TRTTTR
6
TGTTTG

CAAAGKY
7
CAAAGGT

CMSAG
5
CACAG

CCWGGAA
7
CCTGGAA

CACGKG
6
CACGTG

TGGCW
5
TGGCA

AATAAAW
7
AATAAAA

CCCWCCCC
8
CCCTCCCC

TGACCTW
7
TGACCTT


        Random model letter frequencies 
        (from Static_Male-biased_Output/background):
        
A 0.274 C 0.227 G 0.227 T 0.274 

MOTIF	WIDTH	BEST POSSIBLE MATCH
ATYGATY	7	ATTGATT
TRTTTR	6	TGTTTG
CAAAGKY	7	CAAAGGT
CMSAG	5	CACAG
CCWGGAA	7	CCTGGAA
CACGKG	6	CACGTG
TGGCW	5	TGGCA
AATAAAW	7	AATAAAA
CCCWCCCC	8	CCCTCCCC
TGACCTW	7	TGACCTT

SECTION I: HIGH-SCORING MOTIF OCCURRENCES

There were 0 motif occurrences with a p-value less than 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 summing the appropriate entries from each column of the position-dependent scoring matrix that represents the motif.
The table is sorted by increasing p-value.

Motif	Sequence Name	Strand	Start	End	p-value	Matched Sequence

DEBUGGING INFORMATION

Command line:

/share/pkg/meme/4.10.0_4/install/bin/fimo --parse-genomic-coord --verbosity 1 --oc Static_Male-biased_Output/fimo_out_3 --bgfile Static_Male-biased_Output/background --motif TRTTTR Static_Male-biased_Output/dreme_out/dreme.xml Static_Male-biased_Output/Static_Male-biased.fa

Settings:



output directory = Static_Male-biased_Output/fimo_out_3
MEME file name = Static_Male-biased_Output/dreme_out/dreme.xml
sequence file name = Static_Male-biased_Output/Static_Male-biased.fa


background file name = Static_Male-biased_Output/background
allow clobber = true
compute q-values = true


parse genomic coord. = true
text only = false
scan both strands = true


max sequence length = 250000000
output threshold = 0.0001
threshold type = p-value


max stored scores = 100000
pseudocount = 0.1
verbosity = 1


selected motif = TRTTTR

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

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output directory = Static_Male-biased_Output/fimo_out_3	MEME file name = Static_Male-biased_Output/dreme_out/dreme.xml	sequence file name = Static_Male-biased_Output/Static_Male-biased.fa
background file name = Static_Male-biased_Output/background	allow clobber = true	compute q-values = true
parse genomic coord. = true	text only = false	scan both strands = true
max sequence length = 250000000	output threshold = 0.0001	threshold type = p-value
max stored scores = 100000	pseudocount = 0.1	verbosity = 1
selected motif = TRTTTR