Pythium irregulare vs Pythium ultimum Translated Blat Results

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Pythium irregulare (Pythium irregulare DAOM BR486, pir_scaffolds_v1) and Pythium ultimum (Pythium ultimum DAOM BR144, pug) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Pythium irregulare 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: 85,201

Genome coverage (bp) Coding exon coverage (bp)
Pythium irregulare DAOM BR486

Uncovered: 25,970,772 out of 42,968,084
Covered: 16,997,312 out of 42,968,084

Uncovered: 5,987,067 out of 20,543,058
Matches: 11,360,498 out of 20,543,058
Mismatches: 3,175,716 out of 20,543,058
Insertions: 19,777 out of 20,543,058

Pythium ultimum DAOM BR144

Uncovered: 28,973,846 out of 44,913,582
Covered: 15,939,736 out of 44,913,582

Uncovered: 6,495,123 out of 19,826,256
Matches: 10,454,829 out of 19,826,256
Mismatches: 2,863,672 out of 19,826,256
Insertions: 12,632 out of 19,826,256

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 irregulare Pythium ultimum
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}