FIMO Results

FIMO - Motif search tool

FIMO version 5.5.5, (Release date: Thu Sep 14 08:48:04 2023 +1000)

For further information on how to interpret these results please access https://meme-suite.org/meme/doc/fimo-output-format.html.
To get a copy of the FIMO software please access https://meme-suite.org

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 cluster_1_coord_nodup.txt.fa
  
  Database contains 918 sequences, 27540 residues

  MOTIFS streme_out/streme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        1-DCWGRA
        6
        GCTGAA
       
        2-GAAWGGAATC
        10
        GAATGGAATC
       
        3-AAAAAGCAA
        9
        AAAAAGCAA
       
        4-TGGCMW
        6
        TGGCCA
       
Random model letter frequencies (./background):

A 0.311 C 0.189 G 0.189 T 0.311

MOTIF	WIDTH	BEST POSSIBLE MATCH
1-DCWGRA	6	GCTGAA
2-GAAWGGAATC	10	GAATGGAATC
3-AAAAAGCAA	9	AAAAAGCAA
4-TGGCMW	6	TGGCCA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 26 motif occurences with a p-value less than 0.0001. The full set of motif occurences can be seen in the TSV (tab-delimited values) output file fimo.tsv, the GFF3 file fimo.gff which may be suitable for uploading to the UCSC Genome Table Browser (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format), or the XML file fimo.xml.
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.

Motif ID	Alt ID	Sequence Name	Strand	Start	End	p-value	q-value	Matched Sequence
3-AAAAAGCAA	STREME-3	chr7	-	24957544	24957552	1.01e-05	0.101	AAAAAGCAA
3-AAAAAGCAA	STREME-3	chr5	+	51914677	51914685	1.01e-05	0.101	AAAAAGCAA
3-AAAAAGCAA	STREME-3	chr5	+	137371974	137371982	1.01e-05	0.101	aaaaagcaa
3-AAAAAGCAA	STREME-3	chr2	-	198179842	198179850	1.01e-05	0.101	AAAAAGCAA
3-AAAAAGCAA	STREME-3	chr11	-	12315710	12315718	1.62e-05	0.108	AAACAGCAA
3-AAAAAGCAA	STREME-3	chr5	-	32791497	32791505	1.62e-05	0.108	AAACAGCAA
3-AAAAAGCAA	STREME-3	chr3	-	134511362	134511370	2.23e-05	0.127	AAAAGGCAA
3-AAAAAGCAA	STREME-3	chr7	+	15489907	15489915	3.24e-05	0.129	AAAATGCAA
3-AAAAAGCAA	STREME-3	chr7	+	116900934	116900942	3.24e-05	0.129	aaaatgcaa
3-AAAAAGCAA	STREME-3	chr11	+	117324576	117324584	3.24e-05	0.129	AAAATGCAA
3-AAAAAGCAA	STREME-3	chr10	-	95916453	95916461	3.85e-05	0.137	GAAAAGCAA
3-AAAAAGCAA	STREME-3	chr3	-	25519001	25519009	4.46e-05	0.137	AACAAGCAA
3-AAAAAGCAA	STREME-3	chr2	-	150640854	150640862	4.46e-05	0.137	AACAAGCAA
3-AAAAAGCAA	STREME-3	chrX	-	25751932	25751940	5.08e-05	0.143	CAAAAGCAA
3-AAAAAGCAA	STREME-3	chr8	+	79264992	79265000	6.08e-05	0.143	AAATAGCAA
3-AAAAAGCAA	STREME-3	chr2	-	101587260	101587268	6.08e-05	0.143	AAATAGCAA
3-AAAAAGCAA	STREME-3	chr10	+	110957112	110957120	6.08e-05	0.143	AAATAGCAA
3-AAAAAGCAA	STREME-3	chr21	-	36260703	36260711	7.07e-05	0.144	AAACTGCAA
3-AAAAAGCAA	STREME-3	chr11	+	5279184	5279192	7.44e-05	0.144	gaacagcaa
3-AAAAAGCAA	STREME-3	chr2	-	60548192	60548200	8.05e-05	0.144	AAAAAGCCA
3-AAAAAGCAA	STREME-3	chr8	-	31039874	31039882	8.42e-05	0.144	GAAAGGCAA
3-AAAAAGCAA	STREME-3	chr10	+	119225156	119225164	8.42e-05	0.144	GAAAGGCAA
3-AAAAAGCAA	STREME-3	chr18	-	7790155	7790163	9.03e-05	0.144	GAAATGCAA
3-AAAAAGCAA	STREME-3	chr15	-	51598067	51598075	9.03e-05	0.144	GAAATGCAA
3-AAAAAGCAA	STREME-3	chr2	-	88697060	88697068	9.03e-05	0.144	GAAATGCAA
3-AAAAAGCAA	STREME-3	chr6	-	144465658	144465666	9.4e-05	0.144	AACCAGCAA

DEBUGGING INFORMATION

Command line:

fimo --verbosity 1 --oc fimo_out_5 --bgfile ./background --motif 3-AAAAAGCAA streme_out/streme.xml cluster_1_coord_nodup.txt.fa

Settings:


  
    output_directory = fimo_out_5
    MEME file name = streme_out/streme.xml
    sequence file name = cluster_1_coord_nodup.txt.fa
  
  
    background file name = ./background
    alphabet = DNA
    max stored scores = 100000
  
  
    allow clobber = true
    compute q-values = true
    parse genomic coord. = true
  
  
    text only = false
    scan both strands = true
    max strand = false
  
  
    threshold type = p-value
    output theshold = 0.0001
    pseudocount = 0.1
  
  
    alpha = 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 = fimo_out_5	MEME file name = streme_out/streme.xml	sequence file name = cluster_1_coord_nodup.txt.fa
background file name = ./background	alphabet = DNA	max stored scores = 100000
allow clobber = true	compute q-values = true	parse genomic coord. = true
text only = false	scan both strands = true	max strand = false
threshold type = p-value	output theshold = 0.0001	pseudocount = 0.1
alpha = 1	verbosity = 1