Rat vs Zebrafish Translated Blat alignments

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

Configuration parameters

Minimum score (minScore) 30
Database type (t) dnax
Query type (q) dnax
Mask out repeats (mask) lower
Mask out repeats on query (qmask) lower

Results

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