Rat (Rattus norvegicus, RGSC3.4) 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. Rat 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: 181341
| Genome coverage(bp) | Coding exon coverage (bp) | |
|---|---|---|
| Rat |
|
|
| 20,101,554 out of 2,718,897,334 | 15,064,578 out of 33,849,387 | |
| Zebrafish |
|
|
| 14,664,101 out of 1,412,464,843 | 12,262,998 out of 39,233,654 |