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 NEGATIVE.fasta
Database contains 5185 sequences, 129625 residues

MOTIFS ./meme_out/meme.txt (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
WNVAGGADNB 10 ACGAGGAATT

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
WNVAGGADNB MEME-1 Seq5040 - 6 15 1.13e-05 1 ACGAGGAACG
WNVAGGADNB MEME-1 Seq2764 + 7 16 3.58e-05 1 ACAAGGAACT
WNVAGGADNB MEME-1 Seq1536 + 16 25 4.41e-05 1 TCGAGGAACG
WNVAGGADNB MEME-1 Seq3539 - 7 16 7.19e-05 1 ACCAGGAATT
WNVAGGADNB MEME-1 Seq871 - 6 15 7.37e-05 1 TGGAGGAGTT
WNVAGGADNB MEME-1 Seq1152 - 16 25 7.37e-05 1 TGGAGGAGTT
WNVAGGADNB MEME-1 Seq4840 - 13 22 0.000104 1 TTGAGGAATG
WNVAGGADNB MEME-1 Seq915 + 10 19 0.00011 1 ACCAGGAGCT
WNVAGGADNB MEME-1 Seq215 + 10 19 0.000117 1 TCAAGGAACG
WNVAGGADNB MEME-1 Seq4203 - 5 14 0.000117 1 AGAAGGAATG
WNVAGGADNB MEME-1 Seq4363 - 9 18 0.000123 1 ACGAGGATTT
WNVAGGADNB MEME-1 Seq643 - 6 15 0.000147 1 ACGAGGCGTT
WNVAGGADNB MEME-1 Seq4401 + 5 14 0.00016 1 ACCAGGAACG
WNVAGGADNB MEME-1 Seq750 - 5 14 0.00016 1 TCGAGGAGGG
WNVAGGADNB MEME-1 Seq489 - 14 23 0.00016 1 CCGAGGAGTG
WNVAGGADNB MEME-1 Seq4828 + 7 16 0.000183 1 AGAAGGAAAG
WNVAGGADNB MEME-1 Seq4687 + 10 19 0.000189 1 AAGAGGAGAT
WNVAGGADNB MEME-1 Seq4163 + 10 19 0.000195 1 TTAAGGAATT
WNVAGGADNB MEME-1 Seq932 + 8 17 0.000226 1 AGCAGGAGTT
WNVAGGADNB MEME-1 Seq755 - 7 16 0.000232 1 TCAAGGAACC
WNVAGGADNB MEME-1 Seq4143 + 8 17 0.000238 1 ATCAGGAATT
WNVAGGADNB MEME-1 Seq3374 - 14 23 0.000244 1 TCGAGGATTT
WNVAGGADNB MEME-1 Seq3531 + 1 10 0.000252 1 TGAAGGAGAT
WNVAGGADNB MEME-1 Seq4046 - 14 23 0.000252 1 ACGAGGCGAG
WNVAGGADNB MEME-1 Seq1635 + 13 22 0.000261 1 ACGAGGAGAA
WNVAGGADNB MEME-1 Seq1431 + 16 25 0.000261 1 TCAAGGAGGT
WNVAGGADNB MEME-1 Seq3129 - 11 20 0.000273 1 TCCAGGAAAG
WNVAGGADNB MEME-1 Seq219 - 14 23 0.000273 1 TCGAGGCGTT
WNVAGGADNB MEME-1 Seq983 - 14 23 0.000273 1 TCGAGGCGTT
WNVAGGADNB MEME-1 Seq1458 + 10 19 0.000299 1 ACAAGGCGTT
WNVAGGADNB MEME-1 Seq512 - 7 16 0.000316 1 AGCAGGAGAT
WNVAGGADNB MEME-1 Seq2973 + 1 10 0.000323 1 TGAAGGAGCG
WNVAGGADNB MEME-1 Seq5180 - 6 15 0.000329 1 ACAAGGAAGC
WNVAGGADNB MEME-1 Seq4102 + 16 25 0.000339 1 TCAAGGAAGG
WNVAGGADNB MEME-1 Seq3280 - 5 14 0.000347 1 ATGAGGATTT
WNVAGGADNB MEME-1 Seq2729 - 9 18 0.000347 1 ACCAGGAAGT
WNVAGGADNB MEME-1 Seq4823 - 6 15 0.000362 1 TCGAGGAATA
WNVAGGADNB MEME-1 Seq4481 + 12 21 0.000398 1 TCGAGGCGCT
WNVAGGADNB MEME-1 Seq1659 - 8 17 0.000411 1 AAAAGGAACT
WNVAGGADNB MEME-1 Seq4898 - 10 19 0.000411 1 TTGAGGAGGG
WNVAGGADNB MEME-1 Seq806 - 11 20 0.000411 1 AGAAGGAAGT
WNVAGGADNB MEME-1 Seq3156 - 13 22 0.000411 1 ATGAGGATTG
WNVAGGADNB MEME-1 Seq541 - 10 19 0.00042 1 TCGAGGATCG
WNVAGGADNB MEME-1 Seq1421 - 12 21 0.00042 1 AGGAGGATTG
WNVAGGADNB MEME-1 Seq946 + 1 10 0.000429 1 TGCAGGAATT
WNVAGGADNB MEME-1 Seq3460 - 6 15 0.000444 1 ATCAGGAGTC
WNVAGGADNB MEME-1 Seq3247 + 6 15 0.000456 1 ACAAGGCACT
WNVAGGADNB MEME-1 Seq1170 + 10 19 0.000456 1 TCGAGGAGAA
WNVAGGADNB MEME-1 Seq159 - 7 16 0.000456 1 CCAAGGAAAG
WNVAGGADNB MEME-1 Seq440 - 13 22 0.000474 1 AAAAGGAACG
WNVAGGADNB MEME-1 Seq1149 + 13 22 0.000489 1 ACGAGGCACC
WNVAGGADNB MEME-1 Seq287 - 14 23 0.000497 1 AGGAGGATCT
WNVAGGADNB MEME-1 Seq2378 + 16 25 0.000504 1 TCAAGGCGTT
WNVAGGADNB MEME-1 Seq5063 + 10 19 0.000517 1 ATGAGGCGAT
WNVAGGADNB MEME-1 Seq4662 - 5 14 0.000517 1 ACAAGGATTC
WNVAGGADNB MEME-1 Seq4952 - 13 22 0.000517 1 TTCAGGAGAT
WNVAGGADNB MEME-1 Seq3028 + 10 19 0.000547 1 TTCAGGAAAT
WNVAGGADNB MEME-1 Seq2010 + 12 21 0.000547 1 CCAAGGAATC
WNVAGGADNB MEME-1 Seq924 - 8 17 0.000557 1 TGCAGGAAAT
WNVAGGADNB MEME-1 Seq2220 - 14 23 0.000557 1 CTGAGGAGCG
WNVAGGADNB MEME-1 Seq1563 - 14 23 0.000557 1 AAGAGGAGGG
WNVAGGADNB MEME-1 Seq4284 + 5 14 0.000568 1 AACAGGAATT
WNVAGGADNB MEME-1 Seq745 + 11 20 0.000574 1 TGCAGGAACT
WNVAGGADNB MEME-1 Seq2972 - 3 12 0.000574 1 ACGAGGTGCT
WNVAGGADNB MEME-1 Seq4729 - 4 13 0.000594 1 ATAAGGATTT
WNVAGGADNB MEME-1 Seq4185 - 9 18 0.000594 1 AGGAGGCGAG
WNVAGGADNB MEME-1 Seq2189 + 5 14 0.000609 1 ACGAGGTACT
WNVAGGADNB MEME-1 Seq1711 + 10 19 0.000609 1 ATCAGGAAAC
WNVAGGADNB MEME-1 Seq2216 - 5 14 0.000609 1 AGAAGGATTT
WNVAGGADNB MEME-1 Seq2576 + 14 23 0.000609 1 ACGAGGCGGG
WNVAGGADNB MEME-1 Seq923 - 6 15 0.000609 1 AACAGGAGTG
WNVAGGADNB MEME-1 Seq2613 - 7 16 0.000609 1 AGCAGGAGCC
WNVAGGADNB MEME-1 Seq3288 - 14 23 0.000609 1 ATCAGGAAAC
WNVAGGADNB MEME-1 Seq2337 - 7 16 0.000635 1 ATGAGGACTT
WNVAGGADNB MEME-1 Seq49 - 12 21 0.000653 1 TGAAGGAAGT
WNVAGGADNB MEME-1 Seq3736 + 14 23 0.000665 1 ATAAGGCGTT
WNVAGGADNB MEME-1 Seq4989 - 8 17 0.000665 1 ACGAGGAAGA
WNVAGGADNB MEME-1 Seq3630 + 16 25 0.000691 1 TCAAGGCAAT
WNVAGGADNB MEME-1 Seq4775 - 16 25 0.000691 1 TCGAGGCGAC
WNVAGGADNB MEME-1 Seq3820 + 1 10 0.000703 1 ATGAGGCGTC
WNVAGGADNB MEME-1 Seq2182 - 3 12 0.000703 1 TTCAGGAGTC
WNVAGGADNB MEME-1 Seq1885 + 16 25 0.000703 1 AAAAGGAAAC
WNVAGGADNB MEME-1 Seq4019 + 4 13 0.000717 1 TCAAGGCACT
WNVAGGADNB MEME-1 Seq2841 + 7 16 0.000717 1 TCGAGGACAG
WNVAGGADNB MEME-1 Seq3506 - 12 21 0.000717 1 AACAGGAGCT
WNVAGGADNB MEME-1 Seq4478 + 7 16 0.000732 1 CCCAGGAAAT
WNVAGGADNB MEME-1 Seq840 - 4 13 0.000732 1 AACAGGAAAT
WNVAGGADNB MEME-1 Seq2755 + 1 10 0.00076 1 TGCAGGAATC
WNVAGGADNB MEME-1 Seq4841 - 7 16 0.00076 1 TCGAGGATGT
WNVAGGADNB MEME-1 Seq5079 - 14 23 0.00076 1 TCGAGGATGT
WNVAGGADNB MEME-1 Seq1840 - 15 24 0.00076 1 TCGAGGATGT
WNVAGGADNB MEME-1 Seq4757 - 6 15 0.00077 1 TCAAGGCGCG
WNVAGGADNB MEME-1 Seq185 + 12 21 0.000781 1 TCAAGGCAAG
WNVAGGADNB MEME-1 Seq5105 + 16 25 0.000781 1 TCAAGGCAAG
WNVAGGADNB MEME-1 Seq2022 - 8 17 0.000781 1 AGAAGGAGTA
WNVAGGADNB MEME-1 Seq2164 - 11 20 0.000798 1 CAGAGGAATT
WNVAGGADNB MEME-1 Seq2205 - 16 25 0.000798 1 TTGAGGCGAT
WNVAGGADNB MEME-1 Seq1864 - 4 13 0.000813 1 ACCAGGATCG
WNVAGGADNB MEME-1 Seq539 - 5 14 0.000813 1 AACAGGAGCG
WNVAGGADNB MEME-1 Seq3038 + 15 24 0.000813 1 ACCAGGATCG
WNVAGGADNB MEME-1 Seq4345 - 9 18 0.000813 1 AACAGGAGCG
WNVAGGADNB MEME-1 Seq2529 + 3 12 0.000828 1 AACAGGAAAG
WNVAGGADNB MEME-1 Seq2468 + 13 22 0.000828 1 TTGAGGCGCT
WNVAGGADNB MEME-1 Seq3491 - 4 13 0.000828 1 ACGAGGCTTT
WNVAGGADNB MEME-1 Seq3728 - 14 23 0.000828 1 ACGAGGCTTT
WNVAGGADNB MEME-1 Seq4200 - 15 24 0.000828 1 CCCAGGAAAG
WNVAGGADNB MEME-1 Seq887 + 9 18 0.000844 1 TAAAGGAATC
WNVAGGADNB MEME-1 Seq583 - 5 14 0.000844 1 ACGAGGATGC
WNVAGGADNB MEME-1 Seq2473 - 16 25 0.000844 1 TCGAGGACTC
WNVAGGADNB MEME-1 Seq1597 - 11 20 0.000859 1 AGCAGGAAGG
WNVAGGADNB MEME-1 Seq3861 - 13 22 0.000859 1 CTGAGGAAAC
WNVAGGADNB MEME-1 Seq4137 - 13 22 0.000884 1 AGAAGGCGCT
WNVAGGADNB MEME-1 Seq3244 - 9 18 0.000899 1 TCAAGGACTG
WNVAGGADNB MEME-1 Seq593 - 13 22 0.000899 1 ATAAGGATCG
WNVAGGADNB MEME-1 Seq3979 - 13 22 0.000899 1 TCCAGGCGTT
WNVAGGADNB MEME-1 Seq3869 - 16 25 0.000899 1 TCCAGGCGTT
WNVAGGADNB MEME-1 Seq2086 + 10 19 0.000917 1 AGAAGGATCG
WNVAGGADNB MEME-1 Seq2433 - 3 12 0.000917 1 TGGAGGCGAG
WNVAGGADNB MEME-1 Seq2839 - 6 15 0.000917 1 TCAAGGCATC
WNVAGGADNB MEME-1 Seq1807 - 7 16 0.000917 1 ACCAGGACTT
WNVAGGADNB MEME-1 Seq4830 - 8 17 0.000917 1 TTGAGGAGAA
WNVAGGADNB MEME-1 Seq4674 - 8 17 0.000917 1 ACGAGGCGGC
WNVAGGADNB MEME-1 Seq4705 - 2 11 0.000934 1 TTCAGGAAAC
WNVAGGADNB MEME-1 Seq191 + 12 21 0.000934 1 TCCAGGATTG
WNVAGGADNB MEME-1 Seq5130 - 6 15 0.000934 1 ACGAGGCTTG
WNVAGGADNB MEME-1 Seq1992 + 16 25 0.000953 1 TGCAGGAAAC
WNVAGGADNB MEME-1 Seq1759 - 10 19 0.000953 1 CCAAGGAAGG
WNVAGGADNB MEME-1 Seq760 - 11 20 0.000953 1 ATAAGGCGAG
WNVAGGADNB MEME-1 Seq3724 - 16 25 0.000953 1 ACGAGGACGG
WNVAGGADNB MEME-1 Seq3912 + 8 17 0.000969 1 TTGAGGAAAA
WNVAGGADNB MEME-1 Seq4206 - 4 13 0.000987 1 AAGAGGCATG
WNVAGGADNB MEME-1 Seq1500 + 13 22 0.000987 1 ACAAGGCGGG

DEBUGGING INFORMATION

Command line:

fimo --oc fimo_neg -thresh 0.001 ./meme_out/meme.txt NEGATIVE.fasta

Settings:

output_directory = fimo_neg MEME file name = ./meme_out/meme.txt sequence file name = NEGATIVE.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 = 0.001 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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