DNA Sequence Comparer

Step 1

Enter Query Sequence

Query subrange

Step 2

Enter Subject Sequence

Subject subrange

Job Title Enter a descriptive title for this comparison

Step 3

Program Selection

Optimize for

Highly similar sequencesStrict · word size 28 More dissimilar sequencesCross-species · word size 11 Somewhat similar sequencesSensitive · word size 11

Algorithm parameters

Expect threshold Report hits with E-value below this Word size Minimum exact seed match length Max matches per subject Maximum HSPs reported Match/Mismatch scores Reward and penalty per base Gap costs Penalty for insertions/deletions Strand Orientation of the subject

Runs locally, nothing is uploaded

Results

Alignment results

Description	Max Score	Total Score	Query Cover	E value	Per. Ident	Acc. Len	Strand

< 4040 – 5050 – 8080 – 200≥ 200

Color key for alignment scores (bits). Click a bar to open that alignment.

Plus strand match Minus strand match Reported HSP

Subject	HSP	Type	Query pos	Subject pos	Query	Subject	Len

INS position is the query base before the insertion. DEL position is the first deleted query base. Ambiguity codes (N, R, Y…) that are compatible are listed as AMB.

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How it works

Exact local alignment, full report

The query is aligned to every subject on both strands. The method is Smith–Waterman with affine gap costs, so it is exact rather than seed-based. After the best HSP is found, its region is masked and the search repeats, up to the chosen number of HSPs. Program presets use standard nucleotide scoring schemes. The word size is a filter: an HSP must contain an exact run at least that long. Bit scores and E-values use Karlin–Altschul statistics with published λ/K values for each scoring scheme. They are approximate, because there is no length or composition adjustment. Everything runs in a Web Worker in your browser.