| Database and Motifs | High-scoring Motif Occurrences | Debugging Information |
FIMO version 4.10.0, (Release date: Wed May 21 10:35:36 2014 +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.
[full text]
DATABASE
Static_Sex-independent_Output/Static_Sex-independent.fa
Database contains
67058
sequences,
33529000
residues
MOTIFS Static_Sex-independent_Output/dreme_out/dreme.xml (nucleotide)
| MOTIF | WIDTH | BEST POSSIBLE MATCH |
|---|---|---|
| VGGAAR | 6 | AGGAAG |
| RTAAAYA | 7 | GTAAACA |
| RAGKTCA | 7 | AAGGTCA |
| CYCCDCCC | 8 | CCCCTCCC |
| WGCCAR | 6 | AGCCAG |
| ACACRB | 6 | ACACAG |
| CHGGRA | 6 | CTGGGA |
| AGRDGGCG | 8 | AGGGGGCG |
| ARCAAAYA | 8 | AACAAACA |
| TTATYW | 6 | TTATCT |
| AGGHCA | 6 | AGGCCA |
| CACGTG | 6 | CACGTG |
| CYGCCDCC | 8 | CTGCCGCC |
| AATCAWTA | 8 | AATCAATA |
| CARAGTCC | 8 | CAAAGTCC |
| TTAYRYAA | 8 | TTACACAA |
| AAARMAAA | 8 | AAAAAAAA |
| TGACGTMA | 8 | TGACGTCA |
| RGAAAB | 6 | AGAAAG |
| GGGMGGGA | 8 | GGGAGGGA |
| ARAGGGCA | 8 | AGAGGGCA |
| CASAGM | 6 | CAGAGC |
| AAATAY | 6 | AAATAC |
| CCACRYCC | 8 | CCACACCC |
| GCVTGCGY | 8 | GCCTGCGC |
| GTSACAK | 7 | GTGACAG |
| TTTAWW | 6 | TTTAAT |
| CSTCCTCC | 8 | CCTCCTCC |
| CAAAGGTY | 8 | CAAAGGTT |
| CAGGMTG | 7 | CAGGCTG |
| GCDGCMGC | 8 | GCAGCAGC |
| CTGAGYCA | 8 | CTGAGTCA |
| CTGTAAYY | 8 | CTGTAACT |
| STGGCCA | 7 | CTGGCCA |
| MCGTGR | 6 | CCGTGG |
| CTTTRMCC | 8 | CTTTGCCC |
| GATCAATA | 8 | GATCAATA |
| ATGGCGKC | 8 | ATGGCGGC |
| CCBGCCTC | 8 | CCTGCCTC |
| CTGGGYW | 7 | CTGGGCT |
| TTGTGMAA | 8 | TTGTGCAA |
| CVGGGTCA | 8 | CAGGGTCA |
| GTTAATBA | 8 | GTTAATCA |
| CAGCHCCG | 8 | CAGCCCCG |
| AAAGTMCA | 8 | AAAGTACA |
| CGGKGAC | 7 | CGGGGAC |
| AGRTGGCA | 8 | AGATGGCA |
| AAACATTW | 8 | AAACATTT |
| ATKWCATC | 8 | ATGTCATC |
| CCGBAGCC | 8 | CCGCAGCC |
| GCCATGK | 7 | GCCATGG |
| TACADA | 6 | TACAAA |
| GMAAACA | 7 | GCAAACA |
| AGGCDGAG | 8 | AGGCTGAG |
| ATCGATH | 7 | ATCGATC |
| GCTGGRGA | 8 | GCTGGAGA |
| TTAYGAAA | 8 | TTATGAAA |
| CCCGCCC | 7 | CCCGCCC |
| TGKGGACA | 8 | TGGGGACA |
| CCABCTCC | 8 | CCACCTCC |
| CCGVGTCC | 8 | CCGCGTCC |
| TATTGACW | 8 | TATTGACT |
| GATGAYGA | 8 | GATGATGA |
Random model letter frequencies
(from Static_Sex-independent_Output/background):
A 0.241 C 0.259 G 0.259 T 0.241
| Motif | Sequence Name | Strand | Start | End | p-value | Matched Sequence |
|---|
Command line:
/share/pkg/meme/4.10.0_4/install/bin/fimo --parse-genomic-coord --verbosity 1 --oc Static_Sex-independent_Output/fimo_out_17 --bgfile Static_Sex-independent_Output/background --motif CHGGRA Static_Sex-independent_Output/dreme_out/dreme.xml Static_Sex-independent_Output/Static_Sex-independent.fa
Settings:
| output directory = Static_Sex-independent_Output/fimo_out_17 | MEME file name = Static_Sex-independent_Output/dreme_out/dreme.xml | sequence file name = Static_Sex-independent_Output/Static_Sex-independent.fa |
| background file name = Static_Sex-independent_Output/background | allow clobber = true | compute q-values = true |
| parse genomic coord. = true | 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 = 1 |
| selected motif = CHGGRA |
This information can be useful in the event you wish to report a problem with the FIMO software.