Chicken vs Zebra Finch Translated Blat alignments

Chicken (Gallus gallus, WASHUC2) and Zebra Finch (Taeniopygia guttata, taeGut3.2.4) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 53. 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: 3115643

Genome coverage(bp) Coding exon coverage (bp)
Chicken
273,717,294 out of 1,100,480,441 21,463,036 out of 24,644,731
Zebra Finch
261,540,436 out of 1,233,169,488 19,756,100 out of 23,632,257