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_8_coord_nodup.txt.fa
  
  Database contains 967 sequences, 29010 residues

  MOTIFS streme_out/streme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        1-WTCCCAGMHT
        10
        TTCCCAGCAT
       
        2-GTGACTCATH
        10
        GTGACTCATA
       
        3-TCAGMA
        6
        TCAGAA
       
        4-TGCCAAA
        7
        TGCCAAA
       
Random model letter frequencies (./background):

A 0.304 C 0.196 G 0.196 T 0.304

MOTIF	WIDTH	BEST POSSIBLE MATCH
1-WTCCCAGMHT	10	TTCCCAGCAT
2-GTGACTCATH	10	GTGACTCATA
3-TCAGMA	6	TCAGAA
4-TGCCAAA	7	TGCCAAA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 25 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
2-GTGACTCATH	STREME-2	chr18	+	49796310	49796319	1.92e-06	0.0387	GTGACTCATA
2-GTGACTCATH	STREME-2	chr6	-	151437617	151437626	1.92e-06	0.0387	GTGACTCATA
2-GTGACTCATH	STREME-2	chr11	+	11731871	11731880	3.83e-06	0.0463	GTGACTCATG
2-GTGACTCATH	STREME-2	chr14	+	63864486	63864495	4.58e-06	0.0463	GTGAGTCATC
2-GTGACTCATH	STREME-2	chr9	+	5455437	5455446	8.15e-06	0.0659	GTGAGTCATT
2-GTGACTCATH	STREME-2	chr21	+	37374968	37374977	1.01e-05	0.0678	gtgactaatc
2-GTGACTCATH	STREME-2	chr11	-	60097664	60097673	1.3e-05	0.0753	GTGACTAATA
2-GTGACTCATH	STREME-2	chr10	-	92520984	92520993	1.68e-05	0.0847	GTGACTAATT
2-GTGACTCATH	STREME-2	chr9	-	18633061	18633070	2.05e-05	0.0905	GTGACTCACA
2-GTGACTCATH	STREME-2	chr10	+	75230163	75230172	2.24e-05	0.0905	ATGACTCATC
2-GTGACTCATH	STREME-2	chr10	-	24864843	24864852	3.13e-05	0.0924	GTGAGCCATC
2-GTGACTCATH	STREME-2	chr10	+	89553445	89553454	3.31e-05	0.0924	ATGACTCATT
2-GTGACTCATH	STREME-2	chr10	+	95494754	95494763	3.38e-05	0.0924	GTGAGCCATA
2-GTGACTCATH	STREME-2	chr18	+	35014504	35014513	3.57e-05	0.0924	GTGACACATT
2-GTGACTCATH	STREME-2	chr9	-	37251053	37251062	3.81e-05	0.0924	GTAACTCATC
2-GTGACTCATH	STREME-2	chr3	+	195286404	195286413	3.81e-05	0.0924	GTTACTCATC
2-GTGACTCATH	STREME-2	chr12	+	68290651	68290660	4e-05	0.0924	gtgagtgatc
2-GTGACTCATH	STREME-2	chr2	-	18315472	18315481	4.11e-05	0.0924	GTCACTCATT
2-GTGACTCATH	STREME-2	chr17	+	48890699	48890708	6.08e-05	0.129	gtggctcatg
2-GTGACTCATH	STREME-2	chr17	+	35632886	35632895	8.01e-05	0.159	GTGGCCCATA
2-GTGACTCATH	STREME-2	chr9	+	18633062	18633071	8.35e-05	0.159	GTGAGTCACT
2-GTGACTCATH	STREME-2	chr17	+	18646784	18646793	8.66e-05	0.159	GTGACTTATT
2-GTGACTCATH	STREME-2	chr11	+	129960427	129960436	9.33e-05	0.159	gtgactaacc
2-GTGACTCATH	STREME-2	chr22	+	40459766	40459775	9.6e-05	0.159	GGGACTGATA
2-GTGACTCATH	STREME-2	chr3	-	64693037	64693046	9.83e-05	0.159	GTTACTCATG

DEBUGGING INFORMATION

Command line:

fimo --verbosity 1 --oc fimo_out_6 --bgfile ./background --motif 2-GTGACTCATH streme_out/streme.xml cluster_8_coord_nodup.txt.fa

Settings:


  
    output_directory = fimo_out_6
    MEME file name = streme_out/streme.xml
    sequence file name = cluster_8_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_6	MEME file name = streme_out/streme.xml	sequence file name = cluster_8_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