FIMO Results

FIMO - Motif search tool

FIMO version 4.6.1, (Release date: 8 EST 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 
        crp0.fasta

        Database contains 
        18
        sequences,
        1890
        residues
      

        MOTIFS 
        crp0.meme.html 
        (nucleotide)
        


MOTIF
WIDTH

              BEST POSSIBLE MATCH
            


1
18
AATTGTGACGTAGATCAC

1
18
GTGATCTACGTCACAATT

2
8
CGGTGGGG

2
8
CCCCACCG

3
11
CCTGGTGTGCC

3
11
GGCACACCAGG


        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	18	AATTGTGACGTAGATCAC
1	18	GTGATCTACGTCACAATT
2	8	CGGTGGGG
2	8	CCCCACCG
3	11	CCTGGTGTGCC
3	11	GGCACACCAGG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

Each of the following 24 motif occurrences has 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 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 than the end position, the motif occurrence is on the reverse strand.

Motif	Sequence Name	Strand	Start	End	p-value	q-value	Matched Sequence
3	lac	−	33	43	2.27e-07	0.000776	`CCTGGGGTGCC`
1	ara	−	59	76	4.92e-07	0.000591	`AAGTGTGACGCCGTGCAA`
1	lac	+	9	26	4.92e-07	0.000591	`TAATGTGAGTTAGCTCAC`
3	trn9cat	+	36	46	5.03e-07	0.00086	`CCTGGTGTCCC`
1	malt	+	41	58	5.86e-07	0.000591	`AATTGTGACACAGTGCAA`
1	ilv	−	43	60	1.61e-06	0.00106	`AATTGAGGGGTTGATCAC`
1	deop2	+	60	77	1.74e-06	0.00106	`AATTGTGATGTGTATCGA`
1	pbr322	−	57	74	2.98e-06	0.00151	`ATCTGTGCGGTATTTCAC`
1	uxu1	+	17	34	4.31e-06	0.00186	`TGTTGTGATGTGGTTAAC`
1	ce1cg	−	65	82	4.97e-06	0.00188	`TTTTGTGAAAACGATCAA`
1	trn9cat	+	84	101	6.13e-06	0.00206	`AAATGAGACGTTGATCGG`
2	ilv	+	5	12	6.67e-06	0.0235	`CGGCGGGG`
1	gale	−	46	63	8.61e-06	0.00261	`AAGTGTGACATGGAATAA`
1	tnaa	−	75	92	1.05e-05	0.00275	`AAATGTGAATCGAATCAC`
1	crp	−	67	84	1.12e-05	0.00275	`TAATGTGACGTCCTTTGC`
1	cya	+	50	67	1.27e-05	0.00275	`AGGTGTTAAATTGATCAC`
1	male	+	14	31	1.27e-05	0.00275	`TTCTGTAACAGAGATCAC`
2	male	+	41	48	1.48e-05	0.0261	`CGGTGGGG`
1	ompa	+	48	65	1.54e-05	0.00311	`ATGCCTGACGGAGTTCAC`
1	malk	+	61	78	2.09e-05	0.00396	`TTTCGTGATGTTGCTTGC`
1	tdc	−	82	99	2.22e-05	0.00396	`ATATGTGCGACCACTCAC`
1	tnaa	+	71	88	2.5e-05	0.00421	`GATTGTGATTCGATTCAC`
1	tdc	+	78	95	5.8e-05	0.00925	`ATTTGTGAGTGGTCGCAC`
1	bglr1	+	76	93	8.35e-05	0.0126	`AACTGTGAGCATGGTCAT`

DEBUGGING INFORMATION

Command line:

/Users/cegrant/meme/bin/fimo crp0.meme.html crp0.fasta

Settings:



output directory = fimo_out
MEME file name = crp0.meme.html
sequence file name = crp0.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 = crp0.meme.html	sequence file name = crp0.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