Chicken vs C.intestinalis Translated Blat alignments

Chicken (Gallus gallus, WASHUC2) 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 50. 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: 36328

Genome coverage(bp) Coding exon coverage (bp)
Chicken
3,692,180 out of 1,100,480,441 3,248,680 out of 24,644,731
C.intestinalis
2,631,496 out of 173,499,994 2,154,450 out of 16,722,294