Tetrahymena thermophila vs Phaeodactylum tricornutum Translated Blat results

Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) and Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 70. Tetrahymena thermophila was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
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

ParameterTetrahymena thermophilaPhaeodactylum tricornutum
Chunk size1,000,0001,000,000
Overlap10,00010,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 3,599 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Tetrahymena thermophila

Uncovered: 102,570,508 out of 103,014,375
Covered: 443,867 out of 103,014,375

Uncovered: 47,771,863 out of 48,193,658
Matches: 271,216 out of 48,193,658
Mismatches: 150,552 out of 48,193,658
Insertions: 27 out of 48,193,658
Identity over aligned base-pairs: 64.3%

Phaeodactylum tricornutum

Uncovered: 27,276,945 out of 27,568,093
Covered: 291,148 out of 27,568,093

Uncovered: 14,129,708 out of 14,407,044
Matches: 177,435 out of 14,407,044
Mismatches: 99,874 out of 14,407,044
Insertions: 27 out of 14,407,044
Identity over aligned base-pairs: 64.0%