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C.intestinalis vs Lamprey Translated Blat alignments

C.intestinalis (Ciona intestinalis, KH) and Lamprey (Petromyzon marinus, Pmarinus_7.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 66. C.intestinalis 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

C.intestinalis Lamprey
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: 19,086

Genome coverage (bp) Coding exon coverage (bp)
Ciona intestinalis

Uncovered: 113,240,539 out of 115,212,710
Covered: 1,972,171 out of 115,212,710

Uncovered: 14,453,324 out of 16,105,584
Matches: 1,115,007 out of 16,105,584
Mismatches: 537,161 out of 16,105,584
Insertions: 92 out of 16,105,584

Petromyzon marinus

Uncovered: 883,844,673 out of 885,534,757
Covered: 1,690,084 out of 885,534,757

Uncovered: 11,083,417 out of 12,529,983
Matches: 973,968 out of 12,529,983
Mismatches: 472,559 out of 12,529,983
Insertions: 39 out of 12,529,983