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Zebrafish vs C.intestinalis Translated Blat alignments

Zebrafish (Danio rerio, Zv9) and C.intestinalis (Ciona intestinalis, KH) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 66. 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.intestinalis
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: 66,602

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

Uncovered: 1,406,038,253 out of 1,412,464,843
Covered: 6,426,590 out of 1,412,464,843

Uncovered: 37,333,688 out of 42,417,757
Matches: 3,468,753 out of 42,417,757
Mismatches: 1,615,199 out of 42,417,757
Insertions: 117 out of 42,417,757

Ciona intestinalis

Uncovered: 112,172,200 out of 115,212,710
Covered: 3,040,510 out of 115,212,710

Uncovered: 13,609,958 out of 16,105,584
Matches: 1,689,996 out of 16,105,584
Mismatches: 805,401 out of 16,105,584
Insertions: 229 out of 16,105,584