Sequence Length Calculator

Calculator

Sequence input

Paste one sequence, multi-FASTA, or multiple blocks.

Sequence type

Cleaning options

Ignore FASTA headers (>)

Strip whitespace

Force uppercase

Split blocks on blank lines

Counting options

Include gaps (- and .)

Include stop symbol (*)

Allow ambiguous letters

Ungapped length is always reported separately.

Reset

Formula used

This tool counts sequence characters after applying your selected cleaning rules.

Length = number of characters kept after cleaning.
Total length = Σ(length of each sequence).
Average length = total length ÷ number of sequences.
Ungapped length = length after removing - and ..
N50 = length where cumulative sorted lengths reach 50%.
GC% = (G + C) ÷ total length × 100, when applicable.

How to use this calculator

Paste your sequence or multi-FASTA into the input box.
Select Auto-detect or force DNA, RNA, or Protein.
Choose cleaning and counting options for your dataset.
Click Calculate to view results above the form.
Download CSV or PDF for reports and sharing.

Example data table

Illustrative examples to show expected outputs.

Example input	Type	Options	Expected output
`ACGTACGTNN`	DNA	Allow ambiguous letters	Length: 10 • GC%: 40.00 • N: 2
`>seq1\nAUGGCU--AA\n>seq2\nAUGGCUAA`	RNA	Ignore headers, exclude gaps	Sequences: 2 • Total: 16 • Ungapped: 14
`MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPT*`	Protein	Exclude stop symbol	Length equals residues counted without `*`

FAQs

1) Can I paste multi-FASTA sequences?

Yes. Enable “Ignore FASTA headers (>)” to skip header lines. Each record is counted separately for totals, averages, and N50.

2) What is the difference between length and ungapped length?

Length counts all kept symbols after cleaning. Ungapped length removes “-” and “.” so alignment padding does not inflate size.

3) How does auto-detect decide DNA, RNA, or protein?

It checks for U versus T and typical nucleotide alphabets. If the sequence contains many non-nucleotide letters, it switches to protein mode.

4) What does “Allow ambiguous letters” do?

It keeps symbols like N, R, Y for nucleotides, or B, Z, X for proteins. Disable it to restrict counting to strict alphabets.

5) Why does my PDF include fewer sequences than the table?

The PDF exporter is a simple one-page report. Use CSV to export every row for large multi-FASTA datasets.

6) Can I count gaps as part of sequence length?

Yes. Enable “Include gaps (- and .)” to count alignment symbols. Ungapped length is still provided so you can compare both measures.

7) Is my sequence stored anywhere?

No database is used. Results are stored only in your temporary session to generate downloads, and Reset clears the form state.