Sequence Analysis
Multiple Sequence Alignment
Aligns several sequences to reveal conserved regions and how they relate.
Sequences (FASTA)
This is a sample. Click the box to start typing and it will clear.
Examples:
6 protein sequences
Parameters
No alignment yet.
Paste or drop sequences on the left, then press Align.
How to use it
- Paste sequences as FASTA on the left, or drop a file into the box.
- Press Align. The alignment, the consensus and the tree appear together.
- Read the columns: the conserved ones are the point of the exercise, and the summary line says how many sequences and columns you are looking at.
Worth knowing
- Alignment happens in your browser. Nothing you paste is uploaded, and once the page has loaded it makes no network requests at all.
- The summary reports the passes it took and how long it ran, so a slow alignment is visible rather than mysterious.
- An alignment that stops on a repeated tree says so. It means further passes would not change the answer, not that something failed.
Questions
Enough for ordinary bench work — a family of related genes rather than a genome. The summary line reports the time it took, which is the honest guide: if that number is uncomfortable, the input is too big for a browser.
Yes. The scoring matrix follows what you paste.
They are inserted to line the sequences up. Keep them if you pass the alignment to another tool: without them the rows no longer correspond column by column.
The other sequence tools
- FASTA Cleanup — Tidy pasted FASTA and keep the alignment intact.
- DNA Reverse Complement — Reverse, complement, or reverse-complement a nucleotide sequence.
- DNA to Protein Translation — Six-frame translation and open reading frames, in any NCBI genetic code.