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Zebrafish vs Tilapia Translated Blat alignments

Zebrafish (Danio rerio, Zv9) and Tilapia (Oreochromis niloticus, Orenil1.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 67. 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 Tilapia
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: 363,747

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

Uncovered: 1,374,188,328 out of 1,412,464,843
Covered: 38,276,515 out of 1,412,464,843

Uncovered: 16,550,871 out of 42,417,757
Matches: 19,484,482 out of 42,417,757
Mismatches: 6,369,834 out of 42,417,757
Insertions: 12,570 out of 42,417,757

Oreochromis niloticus

Uncovered: 897,441,649 out of 927,383,394
Covered: 29,941,745 out of 927,383,394

Uncovered: 15,718,337 out of 37,304,121
Matches: 16,343,670 out of 37,304,121
Mismatches: 5,223,343 out of 37,304,121
Insertions: 18,771 out of 37,304,121