size -- the size of the ungapped alignment
dt -- the difference between the end of this block and the beginning of
the next block (reference/target sequence)dq -- the difference between the end of this block and the beginning of
the next block (query sequence)NOTE: The last line of the alignment section contains only one number: the ungapped alignment size of the last block.
-Rearrangement display, sometimes called snakes display, is an alternative way to view pairwise alignemnts. +Rearrangement display, sometimes called snakes display, is an alternative way to view pairwise alignments. It is available for PSL and chain format tracks.
Rearrangement display is a representation of the path that the sequence follows in the "other" sequence. You start in the upper left and move to the right, following the lines if you come to the end of a block. If a block is red, which means it is a match on the negative strand, then you reverse your course and start going from right to left. The gray lines mean there are no bases in the other sequence between the blocks. Orange lines means there are some bases in there that are not aligning.
The display type can be enabled on the track configuration page of eligible tracks. Below are two examples for clarity.