On the right hand side, a new tab has been created to show the alignments.
The alignments are organized by query sequence. For each query sequence, a graphical representation of each unique sequence match is shown.
All matches for a query can be shown/hidden by clicking on the small triangle next to the query name. Similarly, clicking on a match header will show/hide the graphical alignment.
It is headed by the list of identical sequence identifiers within the current family and their claimed status (disclosed or claimed). The graphic representation itself is designed to give you a very quick idea about the interest you may have in the match.
It shows all the match’s main scores, alignment coordinates as well as frames or strands.
Here we have a sequence identical in two patent applications (in the same family) and called number 38 in both cases. The sequence is not mentioned in the claims, and thus just disclosed. Clicking on the blue sequence word will pop-up the sequence. The alignment is forward (FW) for both query and subject. The percentage identities over the query, alignment and subject are shown after the frame or strand, as well as the numbers of matches and errors in the alignment, the E-value and Blast score.
It is important to note that the percentage identities are recomputed by Orbit from the alignment found by Blast.
Note that the coordinates are in the original sequence point of view. This means that in cases of, reverse complement (RC, as shown below) or negative frame (-1,-2,-3), the coordinates can go from higher values to lower values and be valid for the nucleotide original sequence even if the sequence has been translated.
The purple triangle on the top left hand corner illustrates the quality of a match. The lighter it is, the less good the match is. By collapsing all hits, it becomes clear which are the good matches (here best is 97%) and poor ones (down to 4%):
From the snapshot above, it is also clear that different HSPs can be clearly seen since identical subject sequences have the same color.