This menu allows searching for sequence motifs and marked sites. The commands in this menu are:
Find Motif: This activates the Find Motif search box. When this box appears, it asks you to enter a motif sequence (a small subsequence of a larger sequence) as the search term. After you enter the search term, the Alignment Explorer finds each occurrence of it and indicates it with yellow highlighting. For example, if you enter the motif “AGA” as the search term, then each occurrence of “AGA” across all sequences in the sequence grid would be highlighted in yellow.
Find Next: This searches for the first occurrence of the motif search term towards the end of the current sequence. If no motif search has been performed prior to clicking this button, the Find Motif search box will appear.
Find Previous: this search towards the beginning of the current sequence for the first occurrence of the motif search term. If no motif search has been performed prior to clicking this button, the Find Motif search box will appear.
Find Marked Site: This locates the marked site in the current sequence. If no site has been marked for this sequence, a warning box will appear.
Highlight Motif: If this item is checked, then all occurrences of the text search term (motif) are highlighted in the alignment grid.