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



FIMO - Motif search tool

FIMO version 5.5.1, (Release date: Sun Jan 29 10:33:12 2023 -0800)

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 prac10_4_nogaps.fasta
Database contains 19 sequences, 12679 residues

MOTIFS results/meme.txt (Protein)

MOTIF WIDTH BEST POSSIBLE MATCH
ILYRGKBY 8 ILYRGKNY
NIHLHWKR 8 NIHLHWKR
KTGGLVIW 8 KTGGLVIW
LKLGRRGV 8 LKLGRRGV

Random model letter frequencies (--nrdb--):
A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058 L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064 W 0.013 Y 0.033


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
ILYRGKBY MEME-1 Q67XL4|reviewed|Uncharacterized/1-444 + 258 265 1.34e-11 1.68e-07 IMYRGKNY
ILYRGKBY MEME-1 Q9FYT6|reviewed|Chloroplastic/1-715 + 648 655 9.74e-11 4.06e-07 ILYRGKNY
ILYRGKBY MEME-1 Q6YYA3|reviewed|Chloroplastic/1-725 + 650 657 9.74e-11 4.06e-07 ILYRGKNY
ILYRGKBY MEME-1 Q0J7J7|reviewed|CRS2-associated/1-366 + 227 234 5.54e-10 1.6e-06 ILYRGRNY
ILYRGKBY MEME-1 Q8L7C2|reviewed|CRM-domain/1-1011 + 663 670 6.4e-10 1.6e-06 IVYRGKNY
ILYRGKBY MEME-1 Q8VYD9|reviewed|CRS2-associated/1-405 + 241 248 8.86e-10 1.73e-06 VLYRGRNY
ILYRGKBY MEME-1 F4JVH1|reviewed|CRM-domain/1-907 + 749 756 9.65e-10 1.73e-06 IVYRGKDY
ILYRGKBY MEME-1 Q657G7|reviewed|CRS2-associated/1-607 + 310 317 1.21e-09 1.9e-06 FLYRGRNY
ILYRGKBY MEME-1 Q6Z4U2|reviewed|CRS2-associated/1-428 + 357 364 2.28e-09 3.17e-06 IVWRGKDY
ILYRGKBY MEME-1 Q8VYD9|reviewed|CRS2-associated/1-405 + 359 366 3e-09 3.75e-06 VIWRGKDY
ILYRGKBY MEME-1 Q9FYT6|reviewed|Chloroplastic/1-715 + 433 440 3.43e-09 3.89e-06 ILYRGKDF
ILYRGKBY MEME-1 Q9LF10|reviewed|Chloroplastic/1-720 + 656 663 3.95e-09 3.89e-06 LIYRGKNY
ILYRGKBY MEME-1 Q9LT57|reviewed|CRM-domain/1-491 + 173 180 4.22e-09 3.89e-06 IMFRGRNY
ILYRGKBY MEME-1 Q9LF10|reviewed|Chloroplastic/1-720 + 442 449 4.66e-09 3.89e-06 VLYRGKDF
ILYRGKBY MEME-1 Q8L7C2|reviewed|CRM-domain/1-1011 + 459 466 4.66e-09 3.89e-06 VLYRGKDF
ILYRGKBY MEME-1 Q6Z4U2|reviewed|CRS2-associated/1-428 + 239 246 6.16e-09 4.82e-06 ILYRGRHY
ILYRGKBY MEME-1 Q6YYA3|reviewed|Chloroplastic/1-725 + 435 442 7.38e-09 5.44e-06 IIYRGKDF
ILYRGKBY MEME-1 A7XN92|reviewed|CRM-domain/1-842 + 668 675 8.98e-09 5.64e-06 VVFRGKNY
ILYRGKBY MEME-1 Q84N48|reviewed|CRS2-associated/1-611 + 314 321 9.81e-09 5.64e-06 FLYRGRHY
ILYRGKBY MEME-1 F4J2U9|reviewed|CRM-domain/1-881 + 504 511 1.03e-08 5.64e-06 VFYRGKNF
ILYRGKBY MEME-1 Q84N49|reviewed|CRS2-associated/1-674 + 265 272 1.04e-08 5.64e-06 FLFRGRNY
ILYRGKBY MEME-1 Q5VMQ5|reviewed|CRS2-associated/1-701 + 265 272 1.04e-08 5.64e-06 FLFRGRNY
ILYRGKBY MEME-1 Q9SL79|reviewed|CRS2-associated/1-701 + 323 330 1.04e-08 5.64e-06 FLFRGRNY
ILYRGKBY MEME-1 Q2R1U8|reviewed|CRM-domain/1-886 + 676 683 1.14e-08 5.93e-06 VVFRGKDY
ILYRGKBY MEME-1 A7XN92|reviewed|CRM-domain/1-842 + 454 461 1.28e-08 6.15e-06 VFYRGKDF
ILYRGKBY MEME-1 Q2R1U8|reviewed|CRM-domain/1-886 + 461 468 1.28e-08 6.15e-06 VFYRGKDF
ILYRGKBY MEME-1 Q8L7C2|reviewed|CRM-domain/1-1011 + 246 253 1.91e-08 8.86e-06 LLYRGVNY
ILYRGKBY MEME-1 F4J2U9|reviewed|CRM-domain/1-881 + 722 729 3.58e-08 1.6e-05 IVYRGQDY
ILYRGKBY MEME-1 A7XN92|reviewed|CRM-domain/1-842 + 249 256 4.83e-08 2.09e-05 SLYRGVDY
ILYRGKBY MEME-1 Q9LDA9|reviewed|CRS2-associated/1-564 + 283 290 6.2e-08 2.59e-05 YLFRGRNY
ILYRGKBY MEME-1 Q9LDA9|reviewed|CRS2-associated/1-564 + 401 408 6.48e-08 2.62e-05 LMWRGREW
ILYRGKBY MEME-1 Q84N49|reviewed|CRS2-associated/1-674 + 383 390 7.45e-08 2.91e-05 LMWRGSDW
ILYRGKBY MEME-1 F4JVH1|reviewed|CRM-domain/1-907 + 504 511 9.22e-08 3.49e-05 VFYRGKSF
ILYRGKBY MEME-1 Q657G7|reviewed|CRS2-associated/1-607 + 428 435 9.48e-08 3.49e-05 LMFRGKEW
ILYRGKBY MEME-1 Q5VMQ5|reviewed|CRS2-associated/1-701 + 383 390 1.27e-07 4.56e-05 LMWRGNDW
ILYRGKBY MEME-1 Q9SL79|reviewed|CRS2-associated/1-701 + 441 448 1.37e-07 4.77e-05 LIWRGREW
ILYRGKBY MEME-1 Q6YYA3|reviewed|Chloroplastic/1-725 + 236 243 1.8e-07 6.09e-05 FVYRGSSY
ILYRGKBY MEME-1 F4J2U9|reviewed|CRM-domain/1-881 + 301 308 2.49e-07 8.19e-05 SLYRGVSY
ILYRGKBY MEME-1 Q84N48|reviewed|CRS2-associated/1-611 + 432 439 2.85e-07 9.15e-05 LMHRGKEW
ILYRGKBY MEME-1 Q9FYT6|reviewed|Chloroplastic/1-715 + 251 258 3.26e-07 0.000102 FVYRGSKY
ILYRGKBY MEME-1 Q6YYA3|reviewed|Chloroplastic/1-725 + 426 433 4.74e-07 0.000145 VILRNKDY
ILYRGKBY MEME-1 Q2R1U8|reviewed|CRM-domain/1-886 + 256 263 4.99e-07 0.000149 SLYRGVAY
ILYRGKBY MEME-1 Q0J7J7|reviewed|CRS2-associated/1-366 + 345 352 7.03e-07 0.000205 ILWRGKVK
ILYRGKBY MEME-1 Q9FYT6|reviewed|Chloroplastic/1-715 + 424 431 9.82e-07 0.000279 VILRNKDF
ILYRGKBY MEME-1 Q8L7C2|reviewed|CRM-domain/1-1011 + 958 965 1.46e-06 0.000405 ILYRGWGA
ILYRGKBY MEME-1 Q0J7J7|reviewed|CRS2-associated/1-366 + 218 225 2.29e-06 0.000624 VIYRNINI
ILYRGKBY MEME-1 F4JVH1|reviewed|CRM-domain/1-907 + 495 502 1.55e-05 0.00413 LLSRNKDF
ILYRGKBY MEME-1 F4JVH1|reviewed|CRM-domain/1-907 + 233 240 4.57e-05 0.0119 VMFRTKSK

DEBUGGING INFORMATION

Command line:

fimo --norc -motif ILYRGKBY results/meme.txt prac10_4_nogaps.fasta

Settings:

output_directory = fimo_out MEME file name = results/meme.txt sequence file name = prac10_4_nogaps.fasta
background file name = --nrdb-- alphabet = Protein max stored scores = 100000
allow clobber = true compute q-values = true parse genomic coord. = false
text only = false scan both strands = false max strand = false
threshold type = p-value output theshold = 0.0001 pseudocount = 0.1
alpha = 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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