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



FIMO - Motif search tool

FIMO version 5.5.0, (Release date: Wed Sep 7 14:18:26 2022 -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 bigclq.txt
Database contains 424 sequences, 6316 residues

MOTIFS streme_out/streme.xml (Protein)

MOTIF WIDTH BEST POSSIBLE MATCH
1-SGSGS 5 SGSGS
2-QGGLPK 6 QGGLPK
3-LEPLJP 6 LEPLIP
4-EPETQB 6 EPETQD

Random model letter frequencies (./background):
A 0.067 C 0.020 D 0.043 E 0.065 F 0.025 G 0.087 H 0.015 I 0.038 K 0.061 L 0.108 M 0.030 N 0.028 P 0.081 Q 0.034 R 0.043 S 0.096 T 0.047 V 0.049 W 0.034 Y 0.029


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence
1-SGSGS STREME-1 GSGSGSGMAVMAPRT + 2 6 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 GSGSGSGMDLVLKRC + 2 6 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 VGSGSGSGMESPSAP + 3 7 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 PGSGSGSGMAPAAWL + 3 7 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 PFGSGSGSGMAVMAP + 4 8 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 HMGSGSGSGMASLSR + 4 8 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 EAGSGSGSGMEEPQS + 4 8 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 CAGSGSGSGMASAGM + 4 8 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 KVGSGSGSGMSPLWW + 4 8 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 LIGSGSGSGMDLVLK + 4 8 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 NYVGSGSGSGMESPS + 5 9 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 VALIGSGSGSGMDLV + 6 10 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 LSHMGSGSGSGMASL + 6 10 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 PDSDGSGSGSGMELA + 6 10 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 NSCAGSGSGSGMASA + 6 10 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 TKNYVGSGSGSGMES + 7 11 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 AAPKKKGSGSGSGMS + 8 12 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 LPLSHMGSGSGSGMA + 8 12 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 LRNSCAGSGSGSGMA + 8 12 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 ELRNPFGSGSGSGMA + 8 12 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 DPEEDDEGSGSGSGM + 9 13 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 KTEGPDSDGSGSGSG + 10 14 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 ISDPEEDDEGSGSGS + 11 15 6.58e-06 0.00102 SGSGS
1-SGSGS STREME-1 SGSWSQKRSFVYVWK + 1 5 9.19e-06 0.00102 SGSWS
1-SGSGS STREME-1 DGGPCPSGSWSQKRS + 7 11 9.19e-06 0.00102 SGSWS
1-SGSGS STREME-1 FPDGGPCPSGSWSQK + 9 13 9.19e-06 0.00102 SGSWS
1-SGSGS STREME-1 CIFPDGGPCPSGSWS + 11 15 9.19e-06 0.00102 SGSWS
1-SGSGS STREME-1 GSGSGMDLVLKRCLL + 2 6 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 GSGSGMYNMMETELK + 2 6 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 GSGSGSGMDLVLKRC + 4 8 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 GSGSGSGMAVMAPRT + 4 8 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 VGSGSGSGMESPSAP + 5 9 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 PGSGSGSGMAPAAWL + 5 9 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 LIGSGSGSGMDLVLK + 6 10 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 KVGSGSGSGMSPLWW + 6 10 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 PFGSGSGSGMAVMAP + 6 10 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 HMGSGSGSGMASLSR + 6 10 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 EAGSGSGSGMEEPQS + 6 10 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 CAGSGSGSGMASAGM + 6 10 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 NYVGSGSGSGMESPS + 7 11 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 VALIGSGSGSGMDLV + 8 12 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 PDSDGSGSGSGMELA + 8 12 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 NSCAGSGSGSGMASA + 8 12 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 LSHMGSGSGSGMASL + 8 12 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 TKNYVGSGSGSGMES + 9 13 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 LPLSHMGSGSGSGMA + 10 14 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 ELRNPFGSGSGSGMA + 10 14 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 LRNSCAGSGSGSGMA + 10 14 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 AAPKKKGSGSGSGMS + 10 14 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 DPEEDDEGSGSGSGM + 11 15 1.12e-05 0.00102 SGSGM
1-SGSGS STREME-1 YASGWGSIEPEEFLT + 3 7 1.36e-05 0.00119 SGWGS
1-SGSGS STREME-1 EPALGTTCYASGWGS + 11 15 1.36e-05 0.00119 SGWGS
1-SGSGS STREME-1 PDSDGSGSGSGMELA + 4 8 1.83e-05 0.00152 DGSGS
1-SGSGS STREME-1 KTEGPDSDGSGSGSG + 8 12 1.83e-05 0.00152 DGSGS
1-SGSGS STREME-1 MFKTEGPDSDGSGSG + 10 14 1.83e-05 0.00152 DGSGS
1-SGSGS STREME-1 RSESGSPSAGGHSKP + 2 6 2.4e-05 0.00195 SESGS

DEBUGGING INFORMATION

Command line:

fimo --parse-genomic-coord --verbosity 1 --oc fimo_out_1 --bgfile ./background --motif 1-SGSGS streme_out/streme.xml bigclq.txt

Settings:

output_directory = fimo_out_1 MEME file name = streme_out/streme.xml sequence file name = bigclq.txt
background file name = ./background alphabet = Protein max stored scores = 100000
allow clobber = true compute q-values = true parse genomic coord. = true
text only = false scan both strands = false 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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