Phytophthora lateralis vs Albugo laibachii Translated Blat results

Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) and Albugo laibachii (Albugo laibachii, ENA1) 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 lateralisAlbugo laibachii
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 27,180 alignment blocks

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

Uncovered: 39,188,017 out of 43,981,379
Covered: 4,793,362 out of 43,981,379

Uncovered: 11,016,055 out of 14,663,433
Matches: 2,424,148 out of 14,663,433
Mismatches: 1,222,499 out of 14,663,433
Insertions: 731 out of 14,663,433
Identity over aligned base-pairs: 66.5%

Albugo laibachii

Uncovered: 29,031,098 out of 32,766,811
Covered: 3,735,713 out of 32,766,811

Uncovered: 12,503,832 out of 15,902,867
Matches: 2,263,259 out of 15,902,867
Mismatches: 1,134,780 out of 15,902,867
Insertions: 996 out of 15,902,867
Identity over aligned base-pairs: 66.6%