Pythium vexans vs Hyaloperonospora arabidopsidis Translated Blat Results

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Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) and Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Pythium vexans 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.


Number of alignment blocks: 40,194

Genome coverage (bp) Coding exon coverage (bp)
Pythium vexans DAOM BR484

Uncovered: 26,203,681 out of 33,844,883
Covered: 7,641,202 out of 33,844,883

Uncovered: 11,780,827 out of 18,608,353
Matches: 4,892,793 out of 18,608,353
Mismatches: 1,932,621 out of 18,608,353
Insertions: 2,112 out of 18,608,353

Hyaloperonospora arabidopsidis

Uncovered: 72,215,019 out of 78,897,814
Covered: 6,682,795 out of 78,897,814

Uncovered: 7,343,965 out of 13,171,834
Matches: 4,199,945 out of 13,171,834
Mismatches: 1,625,624 out of 13,171,834
Insertions: 2,300 out of 13,171,834

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

Pythium vexans Hyaloperonospora arabidopsidis
Chunk size 1,000,000 1,000,000
Overlap 10,000 10,000
Group set size 100,000,000 100,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}