This track displays blastz alignments of the Jan. 2003 rat assembly to the mouse genome, filtered by axtBest and subsetAxt with very stringent constraints as described below.
Each item in the display is identified by the chromosome, strand, and location of the match (in thousands).
For blastz, we use 12 of 19 seeds and then score using:
A C G T A 91 -114 -31 -123 C -114 100 -125 -31 G -31 -125 100 -114 T -123 -31 -114 91 O = 400, E = 30, K = 3000, L = 3000, M = 50
A second pass is done at reduced stringency (7mer seeds and
MSP threshold of K=2200) to attempt to fill in gaps of up to about 10K bp.
Lineage specific repeats are abridged during this alignment.
axtBest
is used to select only the best alignment for any given region of the genome.
subsetAxt is then run on axtBest-filtered alignments
with this matrix:
A C G T A 100 -200 -100 -200 C -200 100 -200 -100 G -100 -200 100 -200 T -200 -100 -200 100
with a gap open penalty of 2000 and a gap extension penalty of 50. The minimum score threshold was 3400.
The track filter can be used to turn on the chromosome color track or to filter the display output by chromosome.