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Mouse vs Medaka BlastZ alignments

Mouse (Mus musculus, NCBIM37) and Medaka(Oryzias latipes, MEDAKA1) were aligned using the BlastZ alignment algorithm (Schwartz S et al., Genome Res.;13(1):103-7, Kent WJ et al., Proc Natl Acad Sci U S A., 2003;100(20):11484-9) in Ensembl release 54. Mouse was used as the reference species. After running BlastZ, the raw BlastZ 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

The alignments were downloaded from UCSC.


Number of alignment blocks: 207963

Genome coverage(bp) Coding exon coverage (bp)
49,333,741 out of 2,716,965,481 22,425,831 out of 35,152,623
34,322,843 out of 868,983,502 17,089,678 out of 30,193,605