If you are using a LANL alignment as your alignment set, your results page will begin with a gene map. The location of your query is shown as a colored bar. Below are the results from the Sample Input for the Conventional QuickAlign.
If you are using your own alignment for another organism, the genome map will not be shown, and your choices will be "Summarize All" and "Summarize by User's Grouping".
"Summarize All" shows a summary of the frequency of all unique sequences in the alignment compared to the input sequence.
In this summary, variations are grouped by species , with a histogram showing the number of mutations relative to the query.
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.
You can force the lines to be longer than 50 characters, by checking "Yes" in the "Display 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.
On the Results page, you will see buttons for "Summarize All" and "Summarize by species ". If you have selected "Calculate frequency by position" as an option, these summaries will include data showing the frequency of each nucleotide or amino acid at each position.
Position Percentage and raw
count of non-gapNon-gap/total
(percentage)Gap/total
(percentage)1 A: 85.39% (1444) T: 14.55% (246) G: 0.06% (1) 1691/1693 (99.88%) 2/1693 (0.12%) 2 T: 99.29% (1680) other: 0.71% (12) 1692/1693 (99.94%) 1/1693 (0.06%) 3 G: 98.11% (1660) other: 1.89% (32) 1692/1693 (99.94%) 1/1693 (0.06%) 4 A: 99.70% (1688) other: 0.30% (5) 1693/1693 (100.00%) 0/1693 (0.00%) 5 A: 85.82% (1452) C: 6.97% (118) G: 3.90% (66) T: 3.31% (56) 1692/1693 (99.94%) 1/1693 (0.06%) 6 A: 94.62% (1600) T: 4.67% (79) other: 0.71% (12) 1691/1693 (99.88%) 2/1693 (0.12%) 7 G: 92.96% (1571) A: 3.96% (67) other: 3.08% (52) 1690/1693 (99.82%) 3/1693 (0.18%) 8 C: 83.04% (1405) T: 16.25% (275) other: 0.71% (12) 1692/1693 (99.94%) 1/1693 (0.06%) 9 A: 80.20% (1357) C: 17.85% (302) other: 1.95% (33) 1692/1693 (99.94%) 1/1693 (0.06%) 10 G: 55.08% (932) C: 25.41% (430) A: 15.25% (258) T: 4.26% (72) 1692/1693 (99.94%) 1/1693 (0.06%) 11 A: 36.98% (626) T: 31.78% (538) G: 29.12% (493) C: 2.13% (36) 1693/1693 (100.00%) 0/1693 (0.00%) 12 C: 79.55% (1346) A: 20.09% (340) other: 0.35% (6) 1692/1693 (99.94%) 1/1693 (0.06%)
If "Calculate frequency by position" is selected, the Summarize pages will also contain links to "See full raw counts", which will show you the full residue counts without applying any cutoff.
Pos A C G T Weight (% non-gap) 1 1444 0 1 246 0.998818665092 2 0 11 1 1680 0.999409332546 3 3 29 1660 0 0.999409332546 4 1688 2 3 0 1.0 5 1452 118 66 56 0.999409332546 6 1600 7 5 79 0.998818665092 7 67 46 1571 6 0.998227997637 8 11 1405 1 275 0.999409332546 9 1357 302 21 12 0.999409332546 10 258 430 932 72 0.999409332546 11 626 36 493 538 1.0 12 340 1346 5 1 0.999409332546
Below the frequency table is a Sequence Logo (frequency graph) that shows a visual representation the frequency of each residue at each position. The height of letters indicates the relative frequency of each residue at each position. The width of a stack of letters is proportional to the fraction of valid residues in that position, i.e., columns with many gaps or unknown residues are narrow. These graphs are produced by WebLogo 3.
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.