Sequence statistics
Length, base composition, GC content and molecular weight, per record and in total.
Length, base composition, GC content and molecular weight, per record and in total.
For the whole input and for every record in it: the number of bases, how often each base occurs and what share of the sequence it is, the GC content, and the molecular weight. It reads plain sequence or FASTA, accepts the IUPAC ambiguity codes, and ignores whitespace and position numbers, so text copied from GenBank or a paper can be pasted as it is.
Each base contributes the mass of its nucleotide residue, and one correction is applied for the ends of the strand:
The single-strand correction of −61.96 g/mol is for a free 5-prime hydroxyl, which is what a synthesised oligonucleotide has. The double-strand correction of +36.04 g/mol is the usual convention for a natural duplex, whose strands carry a 5-prime phosphate. The difference between the two conventions is 79.98 g/mol per strand, below 0.2 % for anything longer than about 50 bases. For RNA the residue masses are A 329.21, C 305.18, G 345.21 and U 306.17. Ambiguity codes are given the mean mass of the bases they stand for, so N in DNA counts as 308.95 g/mol.
"Try an example" loads the 720 nt coding sequence of EGFP and its two sequencing primers,764 nt in three records. The composition is A 179, C 255, G 217, T 113, so the GC content is (255 + 217) ÷ 764 × 100 = 61.8 % and the three strands together weigh235.4 kDa. The EGFP record on its own is 720 nt with A 174, C 240, G 203 and T 103: GC 61.5 %, and a molecular weight of 222.0 kDa as a single strand or 445.0 kDa as a double strand. Those numbers are in the per-record table under Details.
S means G or C and W means A or T, so both can be counted. Every other ambiguity code is left out of the GC calculation and shown on its own row, which keeps an N-rich draft assembly from looking GC-poor. The share of each base in the table is a share of the full length, including ambiguous positions, so those columns add up to 100 %.
For a sliding-window plot of GC along the sequence, use theGC content calculator. For strand asymmetry and the origin of replication, use the GC skew calculator. For primer melting temperature, use the Tm calculator, and for the mass of a given number of moles, thenucleic acid weight and molarity converter.
Add the residue mass of every base (A 313.21, C 289.18, G 329.21, T 304.20 g/mol) and subtract 61.96 for the two ends of a strand with a free 5-prime hydroxyl. A double strand is the sum of both strands plus 36.04, the convention for a natural duplex with 5-prime phosphate ends. RNA uses A 329.21, C 305.18, G 345.21 and U 306.17.
Because of how ambiguous bases are treated. Here S counts as GC, W counts as AT, and every other IUPAC code is left out of the denominator, so a draft sequence full of N is not reported as GC-poor. Tools that divide by the full length give a lower value.
No. Tm depends on salt, oligonucleotide concentration and the nearest-neighbour model, not on composition alone, so it belongs in a calculator of its own. Use the Tm calculator for primers and probes.
Yes. Every record is counted separately and the totals are given for the file. The per-record table is behind Details. Choose a file instead of pasting for anything large; the file is read in your browser and nothing is uploaded.
The IUPAC nucleotide codes A, C, G, T, U and the ambiguity codes R, Y, S, W, K, M, B, D, H, V and N. Whitespace, line breaks and the digits of GenBank-style numbering are ignored. Anything else is reported under the input and left out.