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Zebrafish vs Fugu Translated Blat alignments

Zebrafish (Danio rerio, Zv9) and Fugu (Takifugu rubripes, FUGU4) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 60. Zebrafish 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

Zebrafish Fugu
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: 310,907

Genome coverage (bp) Coding exon coverage (bp)
Danio rerio

Uncovered: 1,378,233,875 out of 1,412,464,843
Covered: 34,230,968 out of 1,412,464,843

Uncovered: 17,435,687 out of 42,417,757
Matches: 18,718,598 out of 42,417,757
Mismatches: 6,251,667 out of 42,417,757
Insertions: 11,805 out of 42,417,757

Takifugu rubripes

Uncovered: 368,107,948 out of 393,312,790
Covered: 25,204,842 out of 393,312,790

Uncovered: 14,534,018 out of 33,921,072
Matches: 14,613,974 out of 33,921,072
Mismatches: 4,759,336 out of 33,921,072
Insertions: 13,744 out of 33,921,072