Pythium irregulare vs Tetrahymena thermophila Translated Blat results

Pythium irregulare (Pythium irregulare DAOM BR486, pir_scaffolds_v1) 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 75. Pythium irregulare 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

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

ParameterPythium irregulareTetrahymena thermophila
Chunk size1,000,0001,000,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 3,091 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium irregulare

Uncovered: 42,526,626 out of 42,968,084
Covered: 441,458 out of 42,968,084

Uncovered: 20,128,134 out of 20,543,058
Matches: 257,676 out of 20,543,058
Mismatches: 157,227 out of 20,543,058
Insertions: 21 out of 20,543,058
Identity over aligned base-pairs: 62.1%

Tetrahymena thermophila

Uncovered: 102,655,339 out of 103,014,375
Covered: 359,036 out of 103,014,375

Uncovered: 47,840,193 out of 48,193,658
Matches: 219,047 out of 48,193,658
Mismatches: 134,365 out of 48,193,658
Insertions: 53 out of 48,193,658
Identity over aligned base-pairs: 62.0%