Codon ChartReverse complement, complement or reverse?
A reverse complement applies base pairing and reverses the order of the input. The reverse complement of 5′-ATGC-3′ is 5′-GCAT-3′: the opposite strand, also written 5′ to 3′. This is the operation usually needed when comparing the opposite strand in a sequence editor or considering a reverse primer.
Choose the operation for the direction you need. All three examples below start with the same 5′-ATGC-3′ input:
| Operation | Result | What changes |
|---|---|---|
| Reverse complement | 5′-GCAT-3′ | Pair the bases and reverse their order. |
| Complement | 3′-TACG-5′ | Pair the bases; keep their left-to-right order. |
| Reverse only | 3′-CGTA-5′ | Reverse the order without pairing the bases. |
The result and FASTA header name the operation and direction. Exchanging these operations can change the interpretation of a primer or sequence match.
Letter case carries through: bases you typed in lowercase, such as a primer tail or restriction site, stay lowercase on the same bases of the result. Copy places the current record's result on your clipboard; Download FASTA saves every record with its original name.
Coding strand, template strand and mRNA
A DNA codon chart uses the coding strand written 5′ to 3′. In this illustrative example, replacing the coding strand's T with U gives the corresponding mRNA sequence:
| Sequence | Direction and bases |
|---|---|
| Coding DNA | 5′-ATG GCT TAA-3′ |
| Template DNA aligned beneath it | 3′-TAC CGA ATT-5′ |
| The same template written 5′ to 3′ | 5′-TTA AGC CAT-3′ |
| Corresponding mRNA | 5′-AUG GCU UAA-3′ |
If the supplied template is TTAAGCCAT written 5′ to 3′, reverse-complement it to recover ATGGCTTAA before looking up the coding-strand codons. If it is TACCGAATT explicitly written 3′ to 5′, complementing it gives the coding sequence in the opposite direction. The starting orientation determines the operation. To go straight from either strand to mRNA and amino acids, use DNA to mRNA.
The RNA/DNA codon comparison explains alphabet switching. A tRNA anticodon is a different triplet; see codon versus anticodon for an RNA pairing example.
Ambiguity letters and RNA
IUPAC ambiguity codes preserve the uncertainty in a base call. R means A or G, and complements to Y, meaning C or T. Likewise, K pairs with M, B with V, and D with H. S, W and N are self-complementary. Reversing a sequence preserves its ambiguity letters; complementing it transforms them according to these pairs.
The nucleotide meanings follow NCBI's IUPAC code reference. Pairing preserves every possible base rather than choosing one:
| DNA symbol | Possible bases | Complement |
|---|---|---|
| R | A or G | Y |
| Y | C or T | R |
| S | C or G | S |
| W | A or T | W |
| K | G or T | M |
| M | A or C | K |
| B | C, G or T | V |
| D | A, G or T | H |
| H | A, C or T | D |
| V | A, C or G | B |
| N | A, C, G or T | N |
For example, ARYN complements to TYRN and reverse-complements to NRYT. RNA output substitutes U for the T. These are nucleotide symbols; the amino-acid alphabet comparison explains why R means arginine in a protein instead.
RNA input is accepted and normalized internally. Choose RNA output to show U instead of T. A mixed T-and-U input is rejected. Paste a plain sequence or up to 100 FASTA records; whitespace and position numbers are ignored. The tool processes up to 30,000 bases total in your browser. Each record is transformed independently, with the original order and names retained.
GC content and next steps
GC percentage uses only definite A, C, G and T bases in its denominator. The result reports how many ambiguous positions were excluded; an entirely ambiguous sequence has no defined percentage here. This is a descriptive sequence calculation, not a melting-temperature estimate. To compare records, inspect GC-rich stretches and save base counts, use the GC content calculator.
For an unambiguous DNA primer, the primer Tm calculator on Plasmid Map makes the sequence and salt assumptions explicit. It estimates a perfectly complementary duplex's melting temperature; it does not check primer binding or specificity. Tm is not a polymerase-specific annealing temperature.
Many restriction enzymes recognize a site that is its own reverse complement. EcoRI's site, GAATTC, reads GAATTC 5′ to 3′ on both strands: reverse-complement it here and the result is unchanged. To find such sites in a whole sequence and see the fragment sizes, use the restriction digest calculator on Plasmid Map.
Download saves every transformed record in FASTA format with its original name, record number and orientation in the header. Use Inspect record or the result arrows to view each output. An empty or invalid record rejects the whole batch; duplicate names remain distinct by record number. To interpret codons on the other strand, continue with six-frame translation. The codon wheel and amino acid chart provide references for reading the resulting assignments.