Parameters Considered When Stitching Hits Having the Same Orientation (Step 4 of the Preprocessing Phase)

To stitch the hits hit1 and hit2, we consider first the distance between them in both organisms (length 1 and 2, respectively). If the segments corresponding to the lengths 1 and 2 are similar, then 1 and 2 are expected to have similar values. Assuming the latter, the difference between the distances of the two hits, i.e., |12 |, should be small. In addition, consecutive hits in similar segments are expected to be close, i.e., both distances, 1 and 2, should be small. Finally, if hit1 and hit2 are stitched (with no other hits stitched to them), we check that the total segment's length in each organism is long enough. In org2 this length is referred to as 3.