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Zebrafish vs C.savignyi Translated Blat alignments

Zebrafish (Danio rerio, Zv9) and C.savignyi (Ciona savignyi, CSAV2.0) 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 C.savignyi
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: 65,261

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

Uncovered: 1,406,166,733 out of 1,412,464,843
Covered: 6,298,110 out of 1,412,464,843

Uncovered: 37,400,514 out of 42,417,757
Matches: 3,446,895 out of 42,417,757
Mismatches: 1,570,176 out of 42,417,757
Insertions: 172 out of 42,417,757

Ciona savignyi

Uncovered: 173,890,161 out of 176,989,013
Covered: 3,098,852 out of 176,989,013

Uncovered: 11,371,130 out of 13,806,906
Matches: 1,661,516 out of 13,806,906
Mismatches: 773,979 out of 13,806,906
Insertions: 281 out of 13,806,906