Currently the only sequence property is a way to adjust where the left edge of the sequence track is, this is so one can align the sequences along some genomic feature.
Under the Edit Menu is "Sequence Properties" which will allow one to adjust the left edge of the track by adding an offset. By default all the sequences treat the start of their sequence as 0 align all the sequences to the left. By using the offset you can enter a positive number to move that many base pair spaces to the right, or a negative number to move that many base pair spaces to the left.
For instance, if you had two sequences, one 5,000 base pairs and the other 10,000 and you wanted to align along the right edge, you could add 5,000 to the first sequence track.