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 
        NC_022103.1.fasta

        Database contains 
        1
        sequences,
        28035
        residues
      

        MOTIFS 
        meme_out2/meme.html 
        (nucleotide)
        


MOTIF
WIDTH

              BEST POSSIBLE MATCH
            


1
11
AACTAGACAAA

2
11
TGTTACAGTTG

3
6
TTCTTG


        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	11	AACTAGACAAA
2	11	TGTTACAGTTG
3	6	TTCTTG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

Each of the following 13 motif occurrences has p-value less then 0.001
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_022103.1	25290	25300	1.96e-06	0.0548
1	NC_022103.1	26219	26229	4.94e-06	0.0692
1	NC_022103.1	24610	24620	1.18e-05	0.11
1	NC_022103.1	61	71	7.55e-05	0.529
1	NC_022103.1	25527	25537	0.000111	0.619
1	NC_022103.1	16688	16698	0.000175	0.808
1	NC_022103.1	20416	20426	0.000206	0.808
1	NC_022103.1	26729	26739	0.000268	0.808
1	NC_022103.1	6989	6999	0.000277	0.808
1	NC_022103.1	3734	3744	0.000288	0.808
1	NC_022103.1	18267	18277	0.000373	0.95
1	NC_022103.1	20326	20336	0.000484	1
1	NC_022103.1	9114	9124	0.000782	1

DEBUGGING INFORMATION

Command line:

fimo --motif 1 --norc --verbosity 1 --output-pthresh 1.0E-3 meme_out2/meme.html NC_022103.1.fasta

Settings:



output directory = fimo_out
MEME file name = meme_out2/meme.html
sequence file name = NC_022103.1.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 = 0.001
pseudocount = 0.1


verbosity = 1
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 = fimo_out	MEME file name = meme_out2/meme.html	sequence file name = NC_022103.1.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 = 0.001	pseudocount = 0.1
verbosity = 1	selected motif = 1	=