Phytophthora lateralis vs Pythium irregulare Translated Blat results

Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) and Pythium irregulare (Pythium irregulare DAOM BR486, pir_scaffolds_v1) 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 lateralisPythium irregulare
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 59,029 alignment blocks

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

Uncovered: 33,611,249 out of 43,981,379
Covered: 10,370,130 out of 43,981,379

Uncovered: 7,166,105 out of 14,663,433
Matches: 5,510,078 out of 14,663,433
Mismatches: 1,983,760 out of 14,663,433
Insertions: 3,490 out of 14,663,433
Identity over aligned base-pairs: 73.5%

Pythium irregulare

Uncovered: 34,413,819 out of 42,968,084
Covered: 8,554,265 out of 42,968,084

Uncovered: 12,765,675 out of 20,543,058
Matches: 5,666,705 out of 20,543,058
Mismatches: 2,106,319 out of 20,543,058
Insertions: 4,359 out of 20,543,058
Identity over aligned base-pairs: 72.9%