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Chicken vs Xenopus Translated Blat alignments

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

Chicken Xenopus
Chunk size 1,000,000 25,000
Overlap 10,000 10,000
Group set size 100,000,000 10,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}


Number of alignment blocks: 191,148

Genome coverage (bp) Coding exon coverage (bp)
Gallus gallus

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

Xenopus tropicalis

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