Zebrafish vs Fugu Translated Blat alignments

Zebrafish (Danio rerio, Zv9) and Fugu (Takifugu rubripes, FUGU4) 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: 310907

Genome coverage(bp) Coding exon coverage (bp)
Zebrafish
34,230,968 out of 1,412,464,843 23,921,899 out of 39,233,654
Fugu
25,204,842 out of 393,312,790 19,387,054 out of 33,921,072