In horizontal view (see Horizontal View) you can enter a sequence motif into the Find Motif field and click Find to check for its presence. (See the figure below.) The general wildcard (*) is not available in this field but most International Union of Pure and Applied Chemistry (IUPAC) nucleotide codes are supported in this field (wsmkrybdhv but not n.-). The number of matches on the positive and negative strand will be displayed on the right side of the Find button and each occurrence of the motif will be highlighted (in green) in the sequence strand that you are displaying, i.e., matches in both strands are not displayed simultaneously. A new horizontal data track is created in the center of the upper panel to display motif matches (Ruler & Motifs track). The matches on different strands are displayed as short vertical bars above (green for the + strand) or below (red for the – strand) the horizontal line.

Sequence view window