Mouse vs X.tropicalis Translated Blat alignments

Mouse (Mus musculus, NCBIM37) and X.tropicalis (Xenopus tropicalis, JGI4.1) 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: 244434

Genome coverage(bp) Coding exon coverage (bp)
Mouse
28,452,389 out of 2,716,965,481 18,136,466 out of 35,152,623
X.tropicalis
20,281,361 out of 1,510,886,836 12,678,022 out of 26,238,419