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Phytophthora infestans vs Hyaloperonospora arabidopsidis Translated Blat results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) 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 70. Phytophthora infestans 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 infestansHyaloperonospora arabidopsidis
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 65,634 alignment blocks

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

Uncovered: 214,520,970 out of 228,543,505
Covered: 14,022,535 out of 228,543,505

Uncovered: 11,300,014 out of 22,421,425
Matches: 8,382,894 out of 22,421,425
Mismatches: 2,732,680 out of 22,421,425
Insertions: 5,837 out of 22,421,425
Identity over aligned base-pairs: 75.4%

Hyaloperonospora arabidopsidis

Uncovered: 68,768,507 out of 78,897,814
Covered: 10,129,307 out of 78,897,814

Uncovered: 4,691,485 out of 13,171,834
Matches: 6,450,793 out of 13,171,834
Mismatches: 2,019,616 out of 13,171,834
Insertions: 9,940 out of 13,171,834
Identity over aligned base-pairs: 76.1%