Explanation of QuickAlign Results

Query Location

The results page begins with a map showing the location (as a small red bar) of your query in the genome.

Summary Table

Below the map a short summary table, colored yellow, appears.

The table shows the query sequence, its length, its location in the genome coordinates of the reference sequence, and the alignment used by QuickAlign. There are three buttons below the table that display three analyses of the alignment. The first two identify and count the variants of your query found in the alignment.

Summarize All

Here is the output for the first button, the summary of variants in the alignment regardless of subtype.

Summarize By Subtype

Here is a sample of the variants grouped by subtype, with a histogram showing the number of mutations relative to the query.

Find Other Matches

The third button searches the reference sequence genome or proteome for other matches to your query sequence. QuickAlign has used the best match as the basis for extracting your alignment, but there may be other good matches across the genome that could be of significance if you are examining potential PCR primers. The "Find Other Matches" button also examines the reverse complement of your sequence for matches. Here is the output.

Alignment

QuickAlign presents its alignment result in "output-aligned" format which looks like this.

For ease of reading the alignment is presented in groups of 10 characters, a space, then 10 more characters, etc. up to a maximum line width of 50 characters. If the query is longer than 50 characters, it will be continued below. However, you can force lines to be longer than 50 characters, by checking "Yes" in the "Do Wide Output Option" on the input page. Sequences identical to the query are highlighted in red. You can download a copy of this alignment in a variety of formats by using the scrolling menu and Download button at the top of the alignment.

Multiple Queries

If you submitted multiple query sequences, the output is slightly different. Only one map is presented that marks the location of each of your sequences. Multiple yellow summary tables are shown together. All the alignments are grouped at the end. There is a link that allows you to jump from the summary table to its corresponding alignment.