Database and Motifs High-scoring Motif Occurences Debugging Information Results in TSV Format Results in GFF3 Format



FIMO - Motif search tool

FIMO version 5.4.1, (Release date: Sat Aug 21 19:23:23 2021 -0700)

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 fimo.fasta
Database contains 100 sequences, 2000 residues

MOTIFS motifs.meme (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
AGGARWA 7 AGGAAAA

Random model letter frequencies (--nrdb--):
A 0.275 C 0.225 G 0.225 T 0.275


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
AGGARWA MEME-1 280 + 9 15 0.000144 0.134 AGGAAAA
AGGARWA MEME-1 204 + 10 16 0.000144 0.134 AGGAAAA
AGGARWA MEME-1 221 + 12 18 0.000289 0.134 AGGAATA
AGGARWA MEME-1 227 + 9 15 0.000526 0.134 AGGAGCA
AGGARWA MEME-1 228 + 9 15 0.000526 0.134 AGGAGCA
AGGARWA MEME-1 229 + 9 15 0.000526 0.134 AGGAGCA
AGGARWA MEME-1 275 + 9 15 0.000526 0.134 AGGAACA
AGGARWA MEME-1 279 + 9 15 0.00108 0.134 AGGTGAA
AGGARWA MEME-1 278 + 9 15 0.00108 0.134 AGGTGAA
AGGARWA MEME-1 252 + 11 17 0.00108 0.134 AGGAGAG
AGGARWA MEME-1 253 + 11 17 0.00108 0.134 AGGAGAG
AGGARWA MEME-1 281 + 12 18 0.00108 0.134 AGGAAAG
AGGARWA MEME-1 215 + 11 17 0.00131 0.134 AGGAATC
AGGARWA MEME-1 216 + 11 17 0.00131 0.134 AGGAATC
AGGARWA MEME-1 203 + 12 18 0.00149 0.134 AAGAGAA
AGGARWA MEME-1 258 + 6 12 0.00164 0.134 TGGAGTA
AGGARWA MEME-1 257 + 6 12 0.00164 0.134 TGGAGTA
AGGARWA MEME-1 256 + 6 12 0.00164 0.134 TGGAGTA
AGGARWA MEME-1 255 + 6 12 0.00164 0.134 TGGAGTA
AGGARWA MEME-1 243 + 9 15 0.00164 0.134 TGGAGTA
AGGARWA MEME-1 300 + 11 17 0.00164 0.134 TGGAGTA
AGGARWA MEME-1 234 + 11 17 0.00173 0.134 AGGAACC
AGGARWA MEME-1 207 + 6 12 0.00188 0.134 AGGAATT
AGGARWA MEME-1 261 + 9 15 0.00188 0.134 AGGAATT
AGGARWA MEME-1 273 + 9 15 0.00188 0.134 AGGAATT
AGGARWA MEME-1 272 + 9 15 0.00188 0.134 AGGAATT
AGGARWA MEME-1 270 + 9 15 0.00188 0.134 AGGAATT
AGGARWA MEME-1 268 + 9 15 0.00188 0.134 AGGAATT
AGGARWA MEME-1 263 + 9 15 0.00188 0.134 AGGAATT
AGGARWA MEME-1 271 + 9 15 0.00188 0.134 AGGAATT
AGGARWA MEME-1 265 + 9 15 0.00188 0.134 AGGAATT
AGGARWA MEME-1 264 + 9 15 0.00188 0.134 AGGAATT
AGGARWA MEME-1 262 + 9 15 0.00188 0.134 AGGAATT
AGGARWA MEME-1 260 + 9 15 0.00188 0.134 AGGAATT
AGGARWA MEME-1 269 + 9 15 0.00188 0.134 AGGAATT
AGGARWA MEME-1 267 + 9 15 0.00188 0.134 AGGAATT
AGGARWA MEME-1 259 + 9 15 0.00188 0.134 AGGAATT
AGGARWA MEME-1 266 + 9 15 0.00188 0.134 AGGAATT
AGGARWA MEME-1 225 + 11 17 0.00214 0.135 AGGAGTG
AGGARWA MEME-1 224 + 11 17 0.00214 0.135 AGGAGTG
AGGARWA MEME-1 223 + 11 17 0.00214 0.135 AGGAGTG
AGGARWA MEME-1 222 + 11 17 0.00214 0.135 AGGAGTG
AGGARWA MEME-1 226 + 11 17 0.00214 0.135 AGGAGTG
AGGARWA MEME-1 235 + 11 17 0.0025 0.154 AGGAGCT
AGGARWA MEME-1 221 + 2 8 0.00339 0.205 TGGAAAT
AGGARWA MEME-1 217 + 5 11 0.00433 0.255 TGGAGTC
AGGARWA MEME-1 230 + 12 18 0.00514 0.297 AGGACAA
AGGARWA MEME-1 229 + 12 18 0.00546 0.297 AGCAATA
AGGARWA MEME-1 228 + 12 18 0.00546 0.297 AGCAATA
AGGARWA MEME-1 227 + 12 18 0.00546 0.297 AGCAATA
AGGARWA MEME-1 240 + 9 15 0.00599 0.319 AAGAGAG
AGGARWA MEME-1 237 + 7 13 0.00792 0.406 TAGAGTA
AGGARWA MEME-1 236 + 7 13 0.00792 0.406 TAGAGTA
AGGARWA MEME-1 233 - 10 16 0.00864 0.419 AAGAATT
AGGARWA MEME-1 232 - 10 16 0.00864 0.419 AAGAATT
AGGARWA MEME-1 231 - 10 16 0.00864 0.419 AAGAATT
AGGARWA MEME-1 206 + 12 18 0.00932 0.434 AGGTGCG
AGGARWA MEME-1 205 + 12 18 0.00932 0.434 AGGTGCG
AGGARWA MEME-1 201 + 2 8 0.00958 0.434 AGCTAAA
AGGARWA MEME-1 277 + 3 9 0.00958 0.434 AGCTAAA

DEBUGGING INFORMATION

Command line:

fimo --oc . --verbosity 1 --thresh 0.01 motifs.meme fimo.fasta

Settings:

output_directory = . MEME file name = motifs.meme sequence file name = fimo.fasta
background file name = --nrdb-- alphabet = DNA max stored scores = 100000
allow clobber = true compute q-values = true parse genomic coord. = false
text only = false scan both strands = true max strand = false
threshold type = p-value output theshold = 0.01 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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