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Mouse vs Rat BlastZ alignments

Mouse (Mus musculus, NCBIM37) and Rat (Rattus norvegicus, RGSC3.4) 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 47. 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

Gap open penalty (O) 400
Gap extend penalty (E) 30
HSP threshold (K) 3000
Threshold for gapped extension (L) 3000
Threshold for alignments between gapped alignment blocks (H) 2000
Masking count (M) 50
Seed and Transition value (T) 2
Scoring matrix (Q) Default


Number of alignment blocks: 1889987

Genome coverage(bp) Coding exon coverage (bp)
1,877,316,536 out of 2,716,965,481 33,991,218 out of 35,152,623
1,726,433,394 out of 2,718,897,334 31,807,586 out of 33,849,387