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Stickleback vs Lamprey Translated Blat alignments

Stickleback (Gasterosteus aculeatus, BROADS1) 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 64. Stickleback 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

Stickleback 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: 95,165

Genome coverage (bp) Coding exon coverage (bp)
Gasterosteus aculeatus

Uncovered: 450,845,909 out of 461,533,448
Covered: 10,687,539 out of 461,533,448

Uncovered: 23,164,919 out of 32,649,418
Matches: 6,974,534 out of 32,649,418
Mismatches: 2,508,572 out of 32,649,418
Insertions: 1,393 out of 32,649,418

Petromyzon marinus

Uncovered: 879,414,927 out of 885,534,757
Covered: 6,119,830 out of 885,534,757

Uncovered: 7,657,452 out of 12,529,983
Matches: 3,548,119 out of 12,529,983
Mismatches: 1,323,147 out of 12,529,983
Insertions: 1,265 out of 12,529,983