Chicken vs Zebrafish Translated Blat alignments

Chicken (Gallus gallus, WASHUC2) 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. Chicken 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: 143148

Genome coverage(bp) Coding exon coverage (bp)
Chicken
16,617,379 out of 1,100,480,441 13,147,920 out of 24,644,731
Zebrafish
14,548,078 out of 1,412,464,843 11,926,266 out of 39,233,654