Mouse vs Chicken Translated Blat alignments

Mouse (Mus musculus, NCBIM37) and Chicken (Gallus gallus, WASHUC2) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 50. Mouse was used as the reference species. After running Translated Blat , the raw Translated Blat alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Full list of pairwise alignments

Configuration parameters

Minimum score (minScore) 30
Database type (t) dnax
Query type (q) dnax
Mask out repeats (mask) lower
Mask out repeats on query (qmask) lower

Results

Number of alignment blocks: 300099

Genome coverage(bp) Coding exon coverage (bp)
Mouse
35,111,027 out of 2,716,965,481 19,675,417 out of 35,152,623
Chicken
27,476,468 out of 1,100,480,441 16,166,431 out of 24,644,731