Sequences

Reference length: 28 bp Mutation rate: 18%

Scoring scheme

Match score: 2 Mismatch penalty: 1 Gap penalty: 2

DP matrix fill

Fill speed: 1.0×

Alignment stats

Matrix size—

Best score cell—

Alignment score—

Aligned length—

Percent identity—

Gaps opened—

The reference sequence is embedded in a longer, noisy "read" flanked by random junk DNA. Smith-Waterman finds the best-scoring local alignment — the mutated core — while ignoring the unrelated flanks, which is exactly what happens when aligning a real sequencing read to a reference genome.