Pythium arrhenomanes vs Paramecium tetraurelia Translated Blat results

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) and Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 75. Pythium arrhenomanes 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

ParameterPythium arrhenomanesParamecium tetraurelia
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 2,648 alignment blocks

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

Uncovered: 44,265,356 out of 44,672,625
Covered: 407,269 out of 44,672,625

Uncovered: 18,001,957 out of 18,367,184
Matches: 222,615 out of 18,367,184
Mismatches: 142,594 out of 18,367,184
Insertions: 18 out of 18,367,184
Identity over aligned base-pairs: 61.0%

Paramecium tetraurelia

Uncovered: 71,730,918 out of 72,094,543
Covered: 363,625 out of 72,094,543

Uncovered: 53,686,453 out of 54,045,570
Matches: 218,504 out of 54,045,570
Mismatches: 140,366 out of 54,045,570
Insertions: 247 out of 54,045,570
Identity over aligned base-pairs: 60.8%