Athanor by arbastro
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How to align two sequences

Select two sequences, or open Object › Chemistry › Align two sequences and paste two sequences or two FASTA records. Press Align to see the identity, gaps, score and the aligned pair.

Steps

  1. Select the two sequences on the page, or choose Main menu › Object › Chemistry › Align two sequences and paste them: two sequences, one per line, or two FASTA records. DNA, RNA or one-letter protein all work.

    Align two sequences with two DNA sequences pasted, one per line.Align two sequences with two DNA sequences pasted, one per line.

  2. Press Align. The result gives the Identity, the Gaps and the Score, then the two sequences aligned, with a bar under each match and a dash at each gap.

    Identity 13/15 (86.7%), Gaps 2/15, Score 9, and the two aligned sequences.Identity 13/15 (86.7%), Gaps 2/15, Score 9, and the two aligned sequences.

  3. Press Copy to copy the alignment as text.

The alignment is global, scored on identity: a match is +1, a mismatch -1 and a gap -2.

BiochemistryHow to build a peptide, DNA or RNA from its sequenceChoose Insert › Build from sequence…, type the one-letter sequence, pick Peptide, DNA or RNA and Residues or Full structure, and press Insert.BiochemistryHow to open a HELM stringPress / for Quick insert, paste a HELM string such as PEPTIDE1{A.C.D.E}$$, and choose Build from HELM. The sequence builder opens with it; press Insert.

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Last updated Nov 12, 2026