Generate a dot plot matrix that visualizes homology between two sequences — each dot marks positions where a short window of residues matches above a configurable stringency threshold. Use this tool to detect direct repeats, inverted repeats, insertions, deletions, and regions of sequence similarity between related genes or genomes. Diagonal lines indicate continuous homology, off-diagonal dots reveal repeats or rearrangements, and the overall density pattern gives an immediate visual impression of the degree and distribution of sequence relatedness.

Features

• Sequence Comparison: Side-by-side comparison of any two sequences
• Adjustable Window: Configurable window size for match sensitivity
• Stringency Control: Set the minimum identity threshold per window
• SVG Output: High-resolution vector dot plot visualization
• Pattern Detection: Identify direct repeats, inversions, and insertions