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Chicken vs Xenopus Translated Blat Results

Chicken (Gallus gallus, Galgal4) and Xenopus (Xenopus tropicalis, JGI_4.2) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 71. 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.

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

Chunking parameters

Chunk size1,000,00025,000
Group set size100,000,00010,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 191,148 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)

Uncovered: 1,023,193,368 out of 1,046,932,099
Covered: 23,738,731 out of 1,046,932,099

Uncovered: 9,591,133 out of 25,934,237
Matches: 12,260,107 out of 25,934,237
Mismatches: 4,075,188 out of 25,934,237
Insertions: 7,809 out of 25,934,237


Uncovered: 1,490,120,648 out of 1,511,717,716
Covered: 21,597,068 out of 1,511,717,716

Uncovered: 15,330,590 out of 30,481,746
Matches: 11,386,417 out of 30,481,746
Mismatches: 3,760,033 out of 30,481,746
Insertions: 4,706 out of 30,481,746