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Phytophthora kernoviae vs Phytophthora infestans Translated Blat Results

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Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) and Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Phytophthora kernoviae 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: 74,795

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora kernoviae 00238/432

Uncovered: 25,223,096 out of 43,208,681
Covered: 17,985,585 out of 43,208,681

Uncovered: 2,447,178 out of 11,508,642
Matches: 7,000,753 out of 11,508,642
Mismatches: 2,047,036 out of 11,508,642
Insertions: 13,675 out of 11,508,642

Phytophthora infestans T30-4

Uncovered: 211,732,124 out of 228,543,505
Covered: 16,811,381 out of 228,543,505

Uncovered: 7,898,682 out of 22,421,425
Matches: 10,987,498 out of 22,421,425
Mismatches: 3,523,609 out of 22,421,425
Insertions: 11,636 out of 22,421,425

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

Phytophthora kernoviae Phytophthora infestans
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}