Chicken vs C.savignyi Translated Blat alignments

Chicken (Gallus gallus, WASHUC2) and C.savignyi (Ciona savignyi, CSAV2.0) 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: 37923

Genome coverage(bp) Coding exon coverage (bp)
Chicken
3,827,100 out of 1,100,480,441 3,286,283 out of 24,644,731
C.savignyi
2,621,533 out of 176,989,013 2,167,403 out of 13,806,906