HalophFGD
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Motif Scan
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FIMO
Paste or upload DNA FASTA (multiple records allowed). Choose a known motif library or upload a custom
.meme
file, set thresholds, and submit to scan.
DNA sequences (paste FASTA / multiple allowed)
Fill example
A/C/G/T/N only. If a file is uploaded, the file content takes precedence.
Or upload FASTA file
Background model (optional)
Auto (estimate base frequencies from inputs)
Use background FASTA to estimate frequencies
Markov model (set order, e.g., 1–2)
Markov order:
0 = zero-order (base frequencies only).
Motif library (.meme)
ArabidopsisDAPv1.meme
ArabidopsisPBM_20140210.meme
JASPAR2022_CORE_plants_redundant_v2.meme
JASPAR2022_CORE_redundant_v2.meme
Or upload a custom motif file (.meme)
Scanner
FIMO (site-level hits with p/q)
MAST (sequence-level characterization)
FIMO is recommended; MAST summarizes per-sequence motif presence.
Significance thresholds
P-value
Q-value (optional)
For FIMO, p-value and q-value filters are both applied if provided.
Strand
Both strands
Forward only (+)
Reverse only (-)
Output limits
Max hits per sequence
Report format
HTML (tables + highlights)
TSV (downloadable)
JSON (programmatic)
Submit scan
Text ≤ 100 lines; file ≤ 300 KB (recommended).
Motif scan task has been submitted