Phytophthora lateralis vs Tetrahymena thermophila Translated Blat results

Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) and Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 76. Phytophthora lateralis 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

ParameterPhytophthora lateralisTetrahymena thermophila
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 2,760 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora lateralis

Uncovered: 43,604,748 out of 43,981,379
Covered: 376,631 out of 43,981,379

Uncovered: 14,332,210 out of 14,663,433
Matches: 206,146 out of 14,663,433
Mismatches: 125,050 out of 14,663,433
Insertions: 27 out of 14,663,433
Identity over aligned base-pairs: 62.2%

Tetrahymena thermophila

Uncovered: 102,703,289 out of 103,014,375
Covered: 311,086 out of 103,014,375

Uncovered: 47,888,540 out of 48,193,658
Matches: 189,847 out of 48,193,658
Mismatches: 115,224 out of 48,193,658
Insertions: 47 out of 48,193,658
Identity over aligned base-pairs: 62.2%