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ORF Finder (Open Reading Frame Finder)
Paste a DNA or RNA sequence to list every open reading frame in all six frames. Set a minimum length, choose ATG-only or alternative start codons and the genetic code, then click any ORF to see its exact coordinates and protein translation.
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ORF map
ORFSelectedStop codon
ORFs
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How to use the ORF Finder (Open Reading Frame Finder)
Paste your DNA (plain, numbered, FASTA or RNA). Spaces and numbers are ignored.
Set the minimum length. 75 nt (25 codons) is a common default; use 300 nt or more to focus on likely genes.
Pick start codons and the genetic code. Use table 11 with alternative starts for bacteria, or table 2 for vertebrate mitochondrial DNA.
Read the map and table. Arrows show each ORF's direction; grey ticks are stop codons in that frame.
Click an ORF to see its protein and coding sequence, then copy it or download every ORF as FASTA or CSV.
How the ORF search works
The tool reads each of the six frames codon by codon. In ATG mode it remembers every start codon it meets and, when it reaches an in-frame stop codon, reports the stretch from the first start to and including the stop (or from every start, if nested ORFs are shown). In stop-to-stop mode every region between two stop codons counts, which is useful for short or unusual genes and for finding the maximum possible coding region. ORFs shorter than the minimum length are dropped.
Coordinates are mapped back to the sequence you pasted. A minus-strand ORF reported as 900 → 478 starts at base 900 and runs leftwards to base 478, so its coding sequence is the reverse complement of bases 478–900.
Start and stop codons in common genetic codes
Genetic code (NCBI table)
Stop codons
Start codons
Used for
1 · Standard
TAA, TAG, TGA
ATG (also CTG, TTG)
Nuclear genes of most eukaryotes
2 · Vertebrate mitochondrial
TAA, TAG, AGA, AGG
ATG, ATA, ATT, ATC, GTG
Human and other vertebrate mtDNA (TGA = Trp)
4 · Mold, protozoan, Mycoplasma
TAA, TAG
ATG, ATA, ATT, ATC, TTA, TTG, CTG, GTG
Mycoplasma, Spiroplasma (TGA = Trp)
5 · Invertebrate mitochondrial
TAA, TAG
ATG, ATA, ATT, ATC, TTG, GTG
Insect and other invertebrate mtDNA
6 · Ciliate nuclear
TGA
ATG
Tetrahymena, Paramecium (TAA, TAG = Gln)
11 · Bacterial and plastid
TAA, TAG, TGA
ATG, GTG, TTG, CTG, ATT, ATC, ATA
Bacteria, archaea, chloroplasts
Tips for spotting real genes
Length matters most. In random DNA with about 50% GC, an ORF longer than about 100 codons is rare, so long ORFs are good gene candidates.
Eukaryotic genes have introns. A genomic sequence may show several short ORFs instead of one long one. Use mRNA or cDNA sequences for eukaryotic genes.
Check the context. Bacterial genes usually have a ribosome binding site (AGGAGG-like) a few bases upstream of the start codon; many eukaryotic mRNAs have a Kozak sequence such as GCCACCATGG.
An open reading frame (ORF) is a stretch of DNA that begins with a start codon, usually ATG, and continues in steps of three bases without interruption until a stop codon (TAA, TAG or TGA in the standard code). Because stop codons are common in random sequence, a long ORF is a strong hint of a protein-coding gene.
Why are there six reading frames?
DNA can be read starting at the first, second or third base, giving three frames on the strand you pasted (+1, +2, +3). The opposite strand is read as the reverse complement, giving three more (−1, −2, −3). Genes can lie on either strand, so all six are searched.
How do I read the start and stop positions?
Positions are 1-based coordinates on the sequence you pasted and include the stop codon. For plus-strand ORFs the start is smaller than the stop. For minus-strand ORFs the start is larger than the stop because the gene runs right to left on your sequence.
What does 'ignore nested ORFs' do?
Several ATGs can sit in frame before the same stop codon. With the option on, only the longest ORF from the first ATG is kept. Turn it off to list every in-frame start as its own ORF, which helps when the true start codon is uncertain.
What minimum ORF length should I use?
A stop codon appears by chance about once every 21 codons in random sequence, so short ORFs are common. 75 nt is a useful default for small genes, 150 to 300 nt removes most chance ORFs, and bacterial genes are typically several hundred codons long.
What are alternative start codons?
Some organisms start translation at codons other than ATG. In bacteria (genetic code 11) GTG and TTG are fairly common starts, and mitochondrial codes allow others such as ATA. The first codon is still translated as methionine when it acts as a start.
Is my sequence uploaded?
No. The whole search runs in your browser, so unpublished sequences never leave your computer.
Are all the tools on FreeToolCabin tested for quality and accuracy?
Yes! Every tool on our site undergoes automated Q/A testing in real browser environments to ensure high precision, correct output, and zero errors. If you happen to spot a bug or have a suggestion, please contact us at [email protected] and our team will review it right away.