Human vs Medaka Translated Blat alignments

Human (Homo sapiens, GRCh37) 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 55. Human 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: 189355

Genome coverage(bp) Coding exon coverage (bp)
Human
20,519,180 out of 3,098,825,702 15,012,710 out of 35,483,623
Medaka
14,902,708 out of 868,983,502 11,956,141 out of 30,193,605