Stickleback vs Zebrafish Translated Blat alignments

Stickleback (Gasterosteus aculeatus, BROADS1) 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. Stickleback 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: 279983

Genome coverage(bp) Coding exon coverage (bp)
Stickleback
31,499,905 out of 461,533,448 22,349,928 out of 32,649,418
Zebrafish
25,998,761 out of 1,412,464,843 19,418,612 out of 39,233,654