Mouse vs Fugu Translated Blat alignments

Mouse (Mus musculus, NCBIM37) 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 50. Mouse 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: 181888

Genome coverage(bp) Coding exon coverage (bp)
Mouse
20,258,466 out of 2,716,965,481 14,914,311 out of 35,152,623
Fugu
14,605,308 out of 393,312,790 12,748,685 out of 33,921,072