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| 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) | |
|---|---|---|
| Mouse |
|
|
| 1,877,316,536 out of 2,716,965,481 | 33,991,218 out of 35,152,623 | |
| Rat |
|
|
| 1,726,433,394 out of 2,718,897,334 | 31,807,586 out of 33,849,387 |