Mouse vs Zebrafish Translated Blat alignments

Mouse (Mus musculus, NCBIM37) and Zebrafish (Danio rerio, Zv9) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 60. 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: 189606

Genome coverage(bp) Coding exon coverage (bp)
Mouse
21,203,840 out of 2,716,965,481 15,390,583 out of 35,152,623
Zebrafish
15,424,354 out of 1,412,464,843 12,846,264 out of 39,233,654