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 
        all.fasta

        Database contains 
        13
        sequences,
        1313
        residues
      

        MOTIFS 
        meme_out/meme.txt 
        (nucleotide)
        


MOTIF
WIDTH

              BEST POSSIBLE MATCH
            


1
11
CTAAACGAACA

1
11
TGTTCGTTTAG

2
50
CTAGGTGTTGGTACCTTCATGAAGGTCACCAAACTGCTGCATTTAGAGAC

2
50
GTCTCTAAATGCAGCAGTTTGGTGACCTTCATGAAGGTACCAACACCTAG

3
8
CTCTTCTG

3
8
CAGAAGAG


        Random model letter frequencies 
        (from non-redundant database):
        
A 0.275 C 0.225 G 0.225 T 0.275 

MOTIF	WIDTH	BEST POSSIBLE MATCH
1	11	CTAAACGAACA
1	11	TGTTCGTTTAG
2	50	CTAGGTGTTGGTACCTTCATGAAGGTCACCAAACTGCTGCATTTAGAGAC
2	50	GTCTCTAAATGCAGCAGTTTGGTGACCTTCATGAAGGTACCAACACCTAG
3	8	CTCTTCTG
3	8	CAGAAGAG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

Each of the following 17 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	NC_004718.3:28030-28130	7	56	9.18e-31	6.05e-28
2	NC_004718.3:28020-28120	17	66	9.18e-31	6.05e-28
1	NC_004718.3:21392-21492	91	101	3.04e-07	0.000208
1	NC_004718.3:27679-27779	91	101	3.04e-07	0.000208
1	NC_004718.3:27764-27864	6	16	3.04e-07	0.000208
1	NC_004718.3:28030-28130	73	83	6.74e-07	0.000277
1	NC_004718.3:28020-28120	83	93	6.74e-07	0.000277
1	NC_004718.3:26298-26398	47	57	9.78e-07	0.000335
1	NC_004718.3:25168-25268	89	99	1.97e-06	0.000578
3	NC_004718.3:21392-21492	15	22	1.47e-05	0.0119
3	NC_004718.3:26298-26398	17	24	1.47e-05	0.0119
3	NC_004718.3:165-265	13	20	1.47e-05	0.0119
1	NC_004718.3:27173-27273	91	101	7.54e-06	0.00194
3	NC_004718.3:26017-26117	1	8	4.4e-05	0.0268
3	NC_004718.3:25168-25268	14	21	7.34e-05	0.0357
1	NC_004718.3:26017-26117	15	25	2.59e-05	0.00593
2	NC_004718.3:28020-28120	54	5	2.75e-05	0.0121

DEBUGGING INFORMATION

Command line:

fimo meme_out/meme.txt all.fasta

Settings:



output directory = fimo_out
MEME file name = meme_out/meme.txt
sequence file name = all.fasta


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


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


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


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


verbosity = 2

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