This part of the window shows the comparison between two sequences. Each red/pink box corresponds to single match, with red representing a good match and white/pale pink a lower scoring match. This view cannot be scrolled directly, instead it tracks the movement of the subject and query sequence views (see the section called The DNA Views).
See 3 to see where this view fits in the main window.
The vertical scrollbar at the right of the view sets the minimum size (in bases on the subject sequence) of the matches that are displayed. The default is 1, so when started ACT will show all matches.
Clicking the left button on a match will highlight the match. Double clicking the mouse on one of the matches will cause the sequence views to align around that match.
Clicking the middle mouse button toggles the locking of the two sequences that are being compared by this comparison view. When locked the sequences will scroll in parallel. When unlocked the sequences can be scrolled independently. (See the section called Notes on Using The Mouse if you do not have a middle mouse button)
The pop-up menu is activated by pressing the third mouse button within the comparison view. The menu items are as follows:
View Selected Matches. Creates a new window which contains a list of currently selected (ie. yellow) matches. Clicking on a match in the list will centre the comparison view on that match.
Flip Query Sequence. Flips the query sequence display so that it appears to be reverse complemented. (See the section called Flip Display.)
Flip Subject Sequence. Flips the subject sequence display so that it appears to be reverse complemented. (See the section called Flip Display.)
Lock Sequences. Lock the two sequences so that they scroll together.
Unlock Sequences. Allow the two sequences to scroll independently.
Set Score Cutoffs ... Pop-up a gadget that allows the matches to be filtered on "score", generally the BLAST score .
Set Percent ID Cutoffs ... Pop-up a gadget that allows the matches to be filtered on the percentage identity.
Offer To RevComp. When this option is "on", double clicking on a reverse complemented match will cause ACT to ask the user whether to flip the query sequence before centering on the match. If "off" the match will just be centred.
Ignore Self Matches. When this option is "on", matches that have the same start and end positions on both the subject and query sequences will not be shown.