GC Content Calculator

Paste a DNA or RNA sequence, or open a FASTA or GenBank file, to get its GC percentage. Multi-FASTA input gets one row per sequence, longer sequences get a sliding-window GC plot, and primers get a Tm and 3′ clamp check.

Runs in your browser. Sequences are not uploaded.

Sequence

1 FASTA sequence, 600 bases. Example: Synthetic sequence with a GC-rich block, to show the sliding-window plot. Paste your own sequence to replace it.

Examples

GC content

52.00%

312 of 600 bases are G or C.

G+C: 31252.00%
A+T: 28848.00%
Ambiguous: 0
Length: 600

A: 154 25.7%
C: 169 28.2%
G: 143 23.8%
T: 134 22.3%

GC profile

GC% in a 50 bp window, moved 5 bp at a time. Blue above 50% marks GC-rich stretches, orange below 50% marks AT-rich ones.

WindowStep

Show window values (111 windows)

Start	End	GC %	GC skew
1	50	48.0%	-0.250
6	55	48.0%	-0.250
11	60	46.0%	-0.304
16	65	46.0%	-0.217
21	70	44.0%	-0.364
26	75	44.0%	-0.364
31	80	46.0%	-0.217
36	85	42.0%	-0.048
41	90	42.0%	-0.048
46	95	40.0%	-0.100
51	100	42.0%	-0.048
56	105	48.0%	-0.083
61	110	46.0%	-0.130
66	115	50.0%	-0.040
71	120	56.0%	0.000
76	125	56.0%	0.000
81	130	54.0%	-0.037
86	135	56.0%	-0.071
91	140	56.0%	-0.143
96	145	52.0%	0.000
101	150	54.0%	-0.185
106	155	54.0%	-0.111
111	160	54.0%	-0.111
116	165	52.0%	-0.231
121	170	52.0%	-0.231
126	175	54.0%	-0.259
131	180	56.0%	-0.214
136	185	56.0%	-0.214
141	190	58.0%	-0.172
146	195	62.0%	-0.226
151	200	62.0%	-0.226
156	205	62.0%	-0.290
161	210	68.0%	-0.294
166	215	72.0%	-0.222
171	220	72.0%	-0.222
176	225	76.0%	-0.105
181	230	80.0%	-0.200
186	235	82.0%	-0.220
191	240	82.0%	-0.220
196	245	82.0%	-0.220
201	250	86.0%	-0.116
206	255	82.0%	-0.073
211	260	82.0%	0.024
216	265	78.0%	0.026
221	270	78.0%	0.026
226	275	76.0%	0.000
231	280	76.0%	0.053
236	285	78.0%	0.077
241	290	78.0%	0.128
246	295	80.0%	0.100
251	300	78.0%	0.128
256	305	84.0%	0.048
261	310	86.0%	-0.070
266	315	86.0%	-0.070
271	320	88.0%	-0.045
276	325	88.0%	-0.091
281	330	86.0%	-0.070
286	335	84.0%	-0.095
291	340	82.0%	-0.122
296	345	84.0%	-0.095
301	350	80.0%	-0.200
306	355	74.0%	-0.135
311	360	68.0%	-0.118
316	365	68.0%	-0.118
321	370	62.0%	-0.161
326	375	56.0%	-0.143
331	380	50.0%	-0.200
336	385	46.0%	-0.043
341	390	42.0%	-0.143
346	395	36.0%	0.000
351	400	38.0%	0.158
356	405	38.0%	0.158
361	410	36.0%	0.222
366	415	36.0%	0.222
371	420	34.0%	0.176
376	425	34.0%	0.176
381	430	34.0%	0.294
386	435	32.0%	0.250
391	440	32.0%	0.375
396	445	30.0%	0.200
401	450	26.0%	0.077
406	455	30.0%	-0.067
411	460	28.0%	0.000
416	465	24.0%	-0.167
421	470	26.0%	-0.077
426	475	26.0%	-0.231
431	480	26.0%	-0.231
436	485	30.0%	-0.200
441	490	30.0%	-0.333
446	495	30.0%	-0.333
451	500	32.0%	-0.250
456	505	28.0%	0.000
461	510	34.0%	0.059
466	515	36.0%	0.000
471	520	38.0%	-0.053
476	525	40.0%	-0.100
481	530	44.0%	-0.182
486	535	38.0%	-0.263
491	540	46.0%	-0.217
496	545	46.0%	-0.130
501	550	46.0%	-0.130
506	555	46.0%	-0.217
511	560	44.0%	-0.182
516	565	42.0%	-0.143
521	570	38.0%	-0.053
526	575	36.0%	0.000
531	580	36.0%	0.111
536	585	38.0%	0.053
541	590	30.0%	0.200
546	595	34.0%	0.294
551	600	32.0%	0.250

How to calculate GC content

GC content is the percentage of bases in a DNA or RNA molecule that are guanine (G) or cytosine (C).

GC content (%) = (G + C) / (A + T + G + C) × 100

For RNA, use U in place of T.

1Count the G and C bases.
2Count every base whose identity is known: A, T (or U), G and C.
3Divide the first count by the second and multiply by 100.

ATGCGGCTTA has 3 G and 2 C, so G + C = 5 out of 10 bases and the GC content is 5 / 10 × 100 = 50%.

How this calculator counts

Line breaks, spaces, line numbers, gap characters (- and .) and FASTA headers are ignored. Lowercase bases count the same as uppercase ones, so soft-masked repeats are included.
S is always G or C, so it counts toward GC. W is always A or T, so it counts toward AT.
N and the other ambiguity codes (R, Y, K, M, B, D, H, V) are left out of both the count and the length. This is the default in Biopython's gc_fraction. When a sequence has ambiguous bases you can switch to weighted counting, where R counts as half a G or C and B as two thirds, or count them in the length.
Anything else, such as * or letters that only appear in protein sequences, is skipped and listed under the input box so it never changes the result silently.

GC content for PCR primers

Most primer design guidelines aim for 40 to 60% GC. In that range a primer binds firmly enough to be specific without being so stable that it anneals to partial matches.

Keep one to three G or C among the last five bases at the 3′ end. This GC clamp holds the end where the polymerase starts, while four or five G or C there make mispriming more likely.
Avoid runs of more than four of the same base, and dinucleotide repeats such as ATATATAT.
Match the two primers of a pair to within about 5 °C Tm. GC content drives Tm, so primers of similar length and GC% usually have similar Tm.

The calculator runs these checks when every sequence you paste is 8 to 60 bases long. Paste a forward and a reverse primer as two FASTA records to see the Tm difference.

Tm uses the basic formula, Tm = 64.9 + 41 × (G + C − 16.4) / N for primers of 14 or more bases and Tm = 2 × (A + T) + 4 × (G + C) for shorter ones, at 50 mM Na+. It is a quick estimate. Nearest-neighbor methods that account for salt and primer concentration are more accurate for final designs.

What counts as high or low GC content

There is no single cutoff. Sequences above about 60% GC are usually called GC-rich and those below about 40% AT-rich. Whole genomes span a wide range.

Approximate genome GC content of common organisms
Organism	Genome GC
Plasmodium falciparum (malaria parasite)	about 19%
Arabidopsis thaliana (thale cress)	about 36%
Saccharomyces cerevisiae (baker's yeast)	about 38%
Homo sapiens (human)	about 41%
Escherichia coli K-12 (lab strain)	about 51%
Streptomyces coelicolor (soil bacterium)	about 72%

G–C pairs form three hydrogen bonds, one more than A–T pairs, and GC-rich stretches also stack more strongly. That is why GC-rich DNA melts at a higher temperature. In the lab this matters in a few places.

PCR. Templates above about 60% GC fold into stable secondary structures and do not fully melt, so they amplify poorly. Additives such as DMSO or betaine and polymerases sold for GC-rich templates help.
Gene synthesis and cloning. Synthesis providers check overall and local GC content. A GC-rich or AT-rich block in the profile plot is worth smoothing with synonymous codons before you order.
Sequencing. Very GC-rich and very AT-rich fragments tend to get lower coverage in short-read libraries. FastQC plots per-sequence GC content for this reason.

Worked examples

Both primers are in the calculator's examples, so you can check every number.

A standard sequencing primer

M13 forward (−20): GTAAAACGACGGCCAGT

1Count the bases: 5 G, 4 C, 6 A and 2 T, 17 in total.
2G + C = 9, so GC content = 9 / 17 × 100 = 52.94%.
3The last five bases, CCAGT, include three G or C, which gives a GC clamp.
4Basic Tm = 64.9 + 41 × (9 − 16.4) / 17 = 47.1 °C.

52.94% GC, inside the 40 to 60% range recommended for primers.

A degenerate primer

16S rRNA primer 27F: AGAGTTTGATCMTGGCTCAG. The M at position 12 means A or C.

1Known bases: 6 G, 3 C, 4 A and 6 T, so G + C = 9 out of 19.
2Leaving M out (the default): 9 / 19 × 100 = 47.37%.
3Weighted, with M counted as 0.5: (9 + 0.5) / 20 × 100 = 47.50%.
4Counting M in the length: 9 / 20 × 100 = 45.00%.

The three conventions differ by up to 2.4 percentage points. Different handling of N and other ambiguity codes is the usual reason two calculators disagree.

Base counts from GC content

In double-stranded DNA every A pairs with a T and every G with a C, so A = T and G = C (Chargaff's rule). One percentage fixes all four bases: G = C = GC% / 2 and A = T = (100 − GC%) / 2.

For example, a 150,000-base stretch of double-stranded DNA that is 64% G+C is 36% A+T, so thymine makes up 18% of the bases: 0.18 × 150,000 = 27,000 thymines. The estimator below starts with these numbers. The rule does not apply to single-stranded DNA or RNA.

Known valuePercentage of all bases

Length (optional)Unit

Base	Share	Count
AAdenine	18%	27,000
TThymine	18%	27,000
GGuanine	32%	48,000
CCytosine	32%	48,000

GC content 64%, 150,000 nucleotides in total.

Related sequence tools

GC content FAQ

What is the formula for GC content?

GC content (%) = (G + C) / (A + T + G + C) × 100. Count the guanine and cytosine bases, divide by the number of bases, and multiply by 100. A 20-base primer with 11 G or C is 55% GC.

What is considered high GC content?

Above about 60% is usually called GC-rich, and below about 40% AT-rich. The human genome averages about 41%. GC-rich templates are harder to amplify by PCR and often need additives such as DMSO or betaine.

What GC content should a primer have?

Aim for 40 to 60%. Also check the 3′ end: one to three G or C among the last five bases helps the primer bind, and more than three raises the risk of mispriming. Keep the two primers of a pair within about 5 °C Tm of each other.

Does the calculator count N or other ambiguous bases?

Not by default. N and the other IUPAC ambiguity codes are left out of both the GC count and the length, the same as Biopython's gc_fraction. S counts as GC and W as AT. When ambiguous bases are present you can switch to weighted counting or count them in the length.

Why does another tool give a different GC%?

Usually because it handles N differently. Some tools divide by the full length including N, which lowers the result. Set ambiguous bases to "Count in length" to match them. Headers, spaces and line numbers do not change the result here.

Can I calculate GC content for RNA?

Yes. U counts in place of T, and the results show A+U instead of A+T when the sequence has U and no T.

Can I check several sequences at once?

Yes. Paste a multi-FASTA, FASTQ reads or a GenBank file, or open one. You get one row per sequence with its length, GC% and counts, plus the combined total, and you can download the table as CSV.

What does the GC profile show?

GC% measured in a window that slides along the sequence. Peaks above 50% are GC-rich stretches and dips below 50% are AT-rich ones. GC skew, (G − C) / (G + C), shows strand bias; in bacterial genomes it changes sign near the origin and terminus of replication.

Is my sequence uploaded anywhere?

No. Parsing and counting run in your browser, and files you open are read locally.