Tetrahymena thermophila vs Hyaloperonospora arabidopsidis Translated Blat Results

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Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) 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. Tetrahymena thermophila 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: 3,819

Genome coverage (bp) Coding exon coverage (bp)
Tetrahymena thermophila

Uncovered: 102,529,666 out of 103,014,375
Covered: 484,709 out of 103,014,375

Uncovered: 47,735,026 out of 48,193,658
Matches: 291,476 out of 48,193,658
Mismatches: 167,087 out of 48,193,658
Insertions: 69 out of 48,193,658

Hyaloperonospora arabidopsidis

Uncovered: 78,566,645 out of 78,897,814
Covered: 331,169 out of 78,897,814

Uncovered: 12,867,277 out of 13,171,834
Matches: 192,260 out of 13,171,834
Mismatches: 112,248 out of 13,171,834
Insertions: 49 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

Tetrahymena thermophila 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}