Zebrafish vs Medaka Translated Blat alignments

Zebrafish (Danio rerio, Zv9) and Medaka (Oryzias latipes, MEDAKA1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 60. Zebrafish 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: 365231

Genome coverage(bp) Coding exon coverage (bp)
Zebrafish
38,969,728 out of 1,412,464,843 24,057,251 out of 39,233,654
Medaka
27,437,647 out of 868,983,502 17,815,874 out of 30,193,605