Display

This track displays repeats from phusion.3 mouse aligned to the human sequence. Each block in the alignment is displayed as a colored block on the track with a line connecting all the blocks in an alignment. The color of each alignment indicates the percent identity of aligned residues over all blocks of the alignment. 50% identity and below is lightly colored and the color gets linearly darker as the percent identity approaches 100%.

Methods

The sequences were aligned with blastz (discontiguous exact seeds, ungapped extension, local alignments via dynamic programming) and postprocessed for single coverage.

Data

human sequence from:

http://genome-test.cse.ucsc.edu/gs.8/oo.33/chromFa.zip

mouse sequence from phusion.3L:

ftp://ftp.ncbi.nlm.nih.gov/pub/TraceDB/mus_musculus/ClipReads/Assemblies/Sanger_Oct15/

repeats from:

http://genome.ucsc.edu/goldenPath/06aug2001/*_rmsk.txt.gz


Aignments contributed by: Scott Schwartz
See http://bio.cse.psu.edu/genome/hummus/2001-12-16/aar/README