Multiple alignment track

Multi-fasta/ClustalW multiple alignment

Multi-fasta data can be displayed on three zoom levels.

  1. Zoomed out: Will show conservation plots.
  2. Medium zoom: Shows conservation as a gray scale. Gaps in the alignment are displayed in red.
  3. Zoomed in: Shows the individual nucleotides. Reference gaps are in yellow, alignment gaps in red . At the bottom of the track, the sequence logo for the aligment is shown.

MAF formatted multiple alignment
Details on the MAF format
Demo video showing the multiple alignment track.
Watch video full screen in HD mode for best quality, the video contains no sound

Multiple alignments can be displayed in three zoom levels.

The most detailed level shows mismatches and gaps for each alignment. Hovering over the track displays the names of the species on the left.

On the middle level, we can still hover the track to see the species. An alignment on the forward strand is drawn in green, one to the reverse strand in blue.

When we zoom even further out, the alignments are displayed in gray. The more species align to a certain part of the reference sequence, the longer the gray line. Individual species are not displayed anymore.

After this, zooming further out will not display alignments anymore because of performance reasons.

Color key:

Gray mismatch with reference
Red gap in alignment
Green Alignment to forward strand
Blue Alignment to reverse strand