Phaeodactylum tricornutum vs Hyaloperonospora arabidopsidis Translated Blat Results

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Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) 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. Phaeodactylum tricornutum 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.

Results

Number of alignment blocks: 6,103

Genome coverage (bp) Coding exon coverage (bp)
Phaeodactylum tricornutum CCAP 1055/1

Uncovered: 26,614,414 out of 27,568,093
Covered: 953,679 out of 27,568,093

Uncovered: 13,509,396 out of 14,407,044
Matches: 588,739 out of 14,407,044
Mismatches: 308,679 out of 14,407,044
Insertions: 230 out of 14,407,044

Hyaloperonospora arabidopsidis

Uncovered: 78,060,595 out of 78,897,814
Covered: 837,219 out of 78,897,814

Uncovered: 12,395,888 out of 13,171,834
Matches: 507,649 out of 13,171,834
Mismatches: 268,167 out of 13,171,834
Insertions: 130 out of 13,171,834

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

Phaeodactylum tricornutum 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}