drag the name of the sequence up or down
When you move the mouse pointer over the label, the pointer will turn into a vertical arrow indicating that the sequence can be moved.
Right-click the name of a sequence | Sort Sequences Alphabetically
If you change the Sequence name (in the Sequence Layout view preferences), you will have to ask the program to sort the sequences again.
Right-click the name of a sequence | Move Sequence to Top
The sequences can also be sorted by similarity, grouping similar sequences together: