## Display

This track displays alignments of the current mouse assembly (phusion.3) against regions of the human genome contained in an ancient copies of transposable elements. In this case "ancient" means that RepeatMasker's annotation indicates that the copy was fixed as an interspersed repeat in a common ancestor of human and mouse. These regions are of interest because they, more likely then any other region, have not been under functional constraint. Each block in the alignment is displayed as a colored block on the track with a line connecting all the blocks. 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%. In the alignments, lower case letters indicate that RepeatMasker annotated them as an interspersed repeat. Because of the high substitution rate in the mouse lineage, the element often only was recognized in the human genome. The original alignments often are much longer, but only the region witin the repeat is displayed.

## 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.3:

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

#### Repeats from:

http://genome.ucsc.edu/goldenPath/06aug2001/database/
(chrN_rmsk.txt.gz for chromosome N)

## Credits

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