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 22 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
1-WTCCCAGMHT	STREME-1	chr8	-	28730855	28730864	7.52e-07	0.0148	TTCCCAGCAT
1-WTCCCAGMHT	STREME-1	chr2	-	240992060	240992069	7.52e-07	0.0148	TTCCCAGCAT
1-WTCCCAGMHT	STREME-1	chr9	+	18633071	18633080	3.23e-06	0.0424	TTCCCAGCAG
1-WTCCCAGMHT	STREME-1	chr10	+	24864860	24864869	9.06e-06	0.0447	atcccagcac
1-WTCCCAGMHT	STREME-1	chr17	-	39178645	39178654	9.06e-06	0.0447	ATCCCAGCAC
1-WTCCCAGMHT	STREME-1	chr17	+	64299198	64299207	9.06e-06	0.0447	atcccagcac
1-WTCCCAGMHT	STREME-1	chr16	-	69531752	69531761	9.06e-06	0.0447	ATCCCAGCAC
1-WTCCCAGMHT	STREME-1	chr9	+	124874443	124874452	9.06e-06	0.0447	atcccagcac
1-WTCCCAGMHT	STREME-1	chr6	+	41367849	41367858	1.34e-05	0.0581	ATCCCAGCCC
1-WTCCCAGMHT	STREME-1	chr3	-	11244338	11244347	1.52e-05	0.0581	TTCCCAGACT
1-WTCCCAGMHT	STREME-1	chr6	+	150867704	150867713	1.62e-05	0.0581	tgcccagcat
1-WTCCCAGMHT	STREME-1	chr11	+	60919508	60919517	3.71e-05	0.122	TGCCCAGCTT
1-WTCCCAGMHT	STREME-1	chr11	-	78467650	78467659	4.11e-05	0.123	TTCCCAGACC
1-WTCCCAGMHT	STREME-1	chr4	-	121826952	121826961	4.36e-05	0.123	CTCCCAGGCT
1-WTCCCAGMHT	STREME-1	chr18	-	23361265	23361274	5.19e-05	0.137	TTCCCTGCTG
1-WTCCCAGMHT	STREME-1	chr20	-	366772	366781	6.1e-05	0.15	TCCCCAGCTC
1-WTCCCAGMHT	STREME-1	chr2	-	183551298	183551307	6.56e-05	0.152	CTCCCAGGTT
1-WTCCCAGMHT	STREME-1	chr9	+	82366780	82366789	7.5e-05	0.161	CTCCCAGATT
1-WTCCCAGMHT	STREME-1	chr11	+	57768880	57768889	7.74e-05	0.161	ATTCCAGCCT
1-WTCCCAGMHT	STREME-1	chr1	-	45945551	45945560	8.55e-05	0.165	TGCCCAGCTG
1-WTCCCAGMHT	STREME-1	chr10	-	29690107	29690116	8.8e-05	0.165	ATCACAGCAT
1-WTCCCAGMHT	STREME-1	chr11	+	24288727	24288736	9.52e-05	0.171	TTCACAGCAG

DEBUGGING INFORMATION

Command line:

fimo --verbosity 1 --oc fimo_out_3 --bgfile ./background --motif 1-WTCCCAGMHT streme_out/streme.xml cluster_8_coord_nodup.txt.fa

Settings:


  
    output_directory = fimo_out_3
    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_3	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