Global Pairwise Sequence Alignment

How to use Global Pairwise Sequence Alignment

Compare two short literal DNA or protein sequences under a clearly stated linear-gap model. The displayed operations consume both original sequences exactly, exposing the selected optimum and tie convention without claiming biological significance or advanced search compatibility.

1. Enter reference sequence, query sequence, match score (1–100), mismatch score (−100–0), per-character gap score (−100–−1).
2. Choose the settings for global pairwise sequence alignment, then run the tool.
3. Review the result and any limitations before copying or downloading it.

Good to know

• 1–200 plain ASCII letters per sequence, at most 40,401 DP cells and a 2-second compute guard. Exact original whole-number score fields; no FASTA headers, whitespace or pre-existing gaps. DNA A/C/G/T/N or standard 20 protein letters plus X.
• Global end-to-end linear-gap alignment only, including penalized end gaps. N/X match only themselves. One optimum uses diagonal/reference-only/query-only tie order. No affine gaps, substitution matrices, local alignment, significance or external alignment-tool compatibility.
• Processing is local. Output is limited to 1,000,000 text characters unless a stricter file limit is stated.