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 
        ../another_species.fasta

        Database contains 
        1
        sequences,
        27996
        residues
      

        MOTIFS 
        ../meme.txt 
        (nucleotide)
        


MOTIF
WIDTH

              BEST POSSIBLE MATCH
            


1
12
TCTCAACTAAAC

2
11
GAGGCTGTTGT

3
11
TGCTAACCATG


        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	12	TCTCAACTAAAC
2	11	GAGGCTGTTGT
3	11	TGCTAACCATG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

Each of the following 19 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
2	KP890336.1	4151	4161	3.95e-07	0.01
2	KP890336.1	26613	26623	6.86e-06	0.0869
2	KP890336.1	15210	15220	1.74e-05	0.146
3	KP890336.1	16095	16105	1.25e-05	0.144
3	KP890336.1	21707	21717	1.62e-05	0.144
3	KP890336.1	23164	23174	1.92e-05	0.144
1	KP890336.1	61	72	1.34e-05	0.192
3	KP890336.1	10471	10481	2.09e-05	0.144
1	KP890336.1	27871	27882	1.57e-05	0.192
2	KP890336.1	4487	4497	6.41e-05	0.174
2	KP890336.1	18064	18074	6.91e-05	0.174
3	KP890336.1	14043	14053	5.46e-05	0.215
3	KP890336.1	26630	26640	5.46e-05	0.215
3	KP890336.1	11133	11143	5.79e-05	0.215
2	KP890336.1	5715	5725	9.88e-05	0.174
2	KP890336.1	6062	6072	9.88e-05	0.174
3	KP890336.1	3078	3088	6.22e-05	0.215
3	KP890336.1	12373	12383	8.42e-05	0.258
1	KP890336.1	9093	9104	9.17e-05	0.605

DEBUGGING INFORMATION

Command line:

fimo --oc . --verbosity 1 --output-pthresh 1.0E-4 --norc ../meme.txt ../another_species.fasta

Settings:



output directory = .
MEME file name = ../meme.txt
sequence file name = ../another_species.fasta


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


compute q-values = true
output p-threshold set = true
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 = 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 = .	MEME file name = ../meme.txt	sequence file name = ../another_species.fasta
background file name = (null)	motif name = motif	allow clobber = true
compute q-values = true	output p-threshold set = true	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 = 1