Phytophthora infestans vs Trypanosoma brucei Translated Blat Results

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Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Phytophthora infestans 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.


Number of alignment blocks: 5,583

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora infestans T30-4

Uncovered: 227,867,084 out of 228,543,505
Covered: 676,421 out of 228,543,505

Uncovered: 21,871,205 out of 22,421,425
Matches: 355,628 out of 22,421,425
Mismatches: 194,469 out of 22,421,425
Insertions: 123 out of 22,421,425

Trypanosoma brucei

Uncovered: 25,385,688 out of 25,789,186
Covered: 403,498 out of 25,789,186

Uncovered: 12,773,971 out of 13,171,744
Matches: 255,773 out of 13,171,744
Mismatches: 141,939 out of 13,171,744
Insertions: 61 out of 13,171,744

Configuration parameters

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 infestans Trypanosoma brucei
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}