Zebrafish vs C.intestinalis Translated Blat alignments

Zebrafish (Danio rerio, Zv9) and C.intestinalis (Ciona intestinalis, JGI2) 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: 65825

Genome coverage(bp) Coding exon coverage (bp)
Zebrafish
6,356,532 out of 1,412,464,843 4,740,558 out of 39,233,654
C.intestinalis
3,048,849 out of 173,499,994 2,429,386 out of 16,722,294