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Phytophthora infestans vs Phaeodactylum tricornutum Translated Blat results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) 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 infestansPhaeodactylum tricornutum
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 9,896 alignment blocks

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

Uncovered: 227,180,057 out of 228,543,505
Covered: 1,363,448 out of 228,543,505

Uncovered: 21,233,779 out of 22,421,425
Matches: 776,997 out of 22,421,425
Mismatches: 410,479 out of 22,421,425
Insertions: 170 out of 22,421,425
Identity over aligned base-pairs: 65.4%

Phaeodactylum tricornutum

Uncovered: 26,645,703 out of 27,568,093
Covered: 922,390 out of 27,568,093

Uncovered: 13,534,756 out of 14,407,044
Matches: 571,416 out of 14,407,044
Mismatches: 300,618 out of 14,407,044
Insertions: 254 out of 14,407,044
Identity over aligned base-pairs: 65.5%