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Phytophthora lateralis vs Phytophthora infestans Translated Blat Results

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Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) 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 lateralis 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: 94,233

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora lateralis MPF4

Uncovered: 24,380,680 out of 43,981,379
Covered: 19,600,699 out of 43,981,379

Uncovered: 3,066,773 out of 14,663,433
Matches: 9,124,865 out of 14,663,433
Mismatches: 2,449,044 out of 14,663,433
Insertions: 22,751 out of 14,663,433

Phytophthora infestans T30-4

Uncovered: 211,033,307 out of 228,543,505
Covered: 17,510,198 out of 228,543,505

Uncovered: 9,298,784 out of 22,421,425
Matches: 10,289,529 out of 22,421,425
Mismatches: 2,814,314 out of 22,421,425
Insertions: 18,798 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 lateralis 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}