Database and Motifs High-scoring Motif Occurences Debugging Information



FIMO - Motif search tool

FIMO version 4.9.1, (Release date: Fri Aug 23 16:49:42 2013 +1000)

For further information on how to interpret these results or to get a copy of the FIMO software please access http://meme.nbcr.net

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.


DATABASE AND MOTIFS

DATABASE crp0.fasta
Database contains 18 sequences, 5670 residues

MOTIFS crp0.meme.html (nucleotide)

MOTIF WIDTH BEST POSSIBLE MATCH
1 18 AATTGTGACGTAGATCAC
2 8 CGGTGGGG
3 11 CCTGGTGTGCC

Random model letter frequencies (from non-redundant database):
A 0.275 C 0.225 G 0.225 T 0.275


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif Sequence Name Strand Start End p-value q-value Matched Sequence
3 lac 33 43 1.13e-07 0.000388 CCTGGGGTGCC
1 lac + 9 26 4.53e-07 0.000654 TAATGTGAGTTAGCTCAC
1 ara 59 76 4.91e-07 0.000654 AAGTGTGACGCCGTGCAA
3 trn9cat + 36 46 5.03e-07 0.00086 CCTGGTGTCCC
1 malt + 41 58 6.49e-07 0.000654 AATTGTGACACAGTGCAA
1 deop2 + 60 77 1.7e-06 0.00106 AATTGTGATGTGTATCGA
1 ilv 43 60 1.75e-06 0.00106 AATTGAGGGGTTGATCAC
1 pbr322 57 74 2.97e-06 0.0015 ATCTGTGCGGTATTTCAC
1 uxu1 + 17 34 3.9e-06 0.00168 TGTTGTGATGTGGTTAAC
1 ce1cg 65 82 4.57e-06 0.00173 TTTTGTGAAAACGATCAA
1 trn9cat + 84 101 6.27e-06 0.00211 AAATGAGACGTTGATCGG
2 ilv + 5 12 6.67e-06 0.0235 CGGCGGGG
1 gale 46 63 8.7e-06 0.00253 AAGTGTGACATGGAATAA
1 tnaa 75 92 9.72e-06 0.00253 AAATGTGAATCGAATCAC
1 crp 67 84 1.01e-05 0.00253 TAATGTGACGTCCTTTGC
1 male + 14 31 1.18e-05 0.00268 TTCTGTAACAGAGATCAC
1 cya + 50 67 1.24e-05 0.00268 AGGTGTTAAATTGATCAC
2 male + 41 48 1.48e-05 0.0261 CGGTGGGG
1 ompa + 48 65 1.52e-05 0.00307 ATGCCTGACGGAGTTCAC
1 malk + 61 78 1.85e-05 0.0035 TTTCGTGATGTTGCTTGC
1 tdc 82 99 2e-05 0.00355 ATATGTGCGACCACTCAC
1 tnaa + 71 88 2.37e-05 0.00398 GATTGTGATTCGATTCAC
1 tdc + 78 95 5.68e-05 0.00904 ATTTGTGAGTGGTCGCAC
1 bglr1 + 76 93 8.97e-05 0.0136 AACTGTGAGCATGGTCAT

DEBUGGING INFORMATION

Command line:

fimo --oc fimo_example_output_files crp0.meme.html crp0.fasta

Settings:

output directory = fimo_example_output_files MEME file name = crp0.meme.html sequence file name = crp0.fasta
allow clobber = true compute q-values = true parse genomic coord. = false
text only = false scan both strands = true max sequence length = 250000000
output threshold = 0.0001 threshold type = p-value max stored scores = 100000
pseudocount = 0.1 verbosity = 2 =

This information can be useful in the event you wish to report a problem with the FIMO software.


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