Locate approximate matches between a DNA target and query sequence using customizable scoring penalties.
Raw or FASTA sequence to search (limit 2,000,000 characters). Non-DNA symbols are stripped before scoring.
DNA query motif (limit 30 characters).
Paste your target DNA sequence (up to 2 million characters) and a query sequence (up to 30 characters). Non-DNA characters are automatically removed.
Set match score (reward for identical bases), mismatch score (penalty for substitutions), and gap penalty (cost for insertions/deletions). Higher match scores favor exact matches.
Choose how many top-scoring approximate matches to report (1-40). The algorithm iteratively finds high-scoring alignments and removes matched regions between iterations.
Review the aligned segments showing query positions, target positions, and alignment scores. Gaps are marked with dashes in the output.
Positive match scores reward identical bases; negative mismatch scores penalize substitutions. Values are applied exactly as in the legacy tool.
Gap values are subtracted when insertions or deletions occur (positive values create penalties, negative values reward gaps).
The search iteratively reports up to the requested number of highest scoring alignments, removing matched regions between iterations.