Mouse (Mus musculus, NCBIM37) and Chicken (Gallus gallus, WASHUC2) 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| Minimum score (minScore) | 30 |
| Database type (t) | dnax |
| Query type (q) | dnax |
| Mask out repeats (mask) | lower |
| Mask out repeats on query (qmask) | lower |
Number of alignment blocks: 300099
| Genome coverage(bp) | Coding exon coverage (bp) | |
|---|---|---|
| Mouse |
|
|
| 35,111,027 out of 2,716,965,481 | 19,675,417 out of 35,152,623 | |
| Chicken |
|
|
| 27,476,468 out of 1,100,480,441 | 16,166,431 out of 24,644,731 |