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Human vs Stickleback Translated Blat alignments

Human (Homo sapiens, GRCh37) and Stickleback (Gasterosteus aculeatus, BROADS1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl release 55. Human 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

Human Stickleback
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}


Number of alignment blocks: 189,249

Genome coverage (bp) Coding exon coverage (bp)
Homo sapiens

Uncovered: 3,078,204,329 out of 3,098,825,702
Covered: 20,621,373 out of 3,098,825,702

Uncovered: 20,238,347 out of 35,313,516
Matches: 11,002,121 out of 35,313,516
Mismatches: 4,068,123 out of 35,313,516
Insertions: 4,925 out of 35,313,516

Gasterosteus aculeatus

Uncovered: 446,407,298 out of 461,533,448
Covered: 15,126,150 out of 461,533,448

Uncovered: 19,691,803 out of 32,649,418
Matches: 9,453,331 out of 32,649,418
Mismatches: 3,498,807 out of 32,649,418
Insertions: 5,477 out of 32,649,418