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Tetrahymena thermophila vs Phytophthora infestans Translated Blat Results

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Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) 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. 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: 5,300

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

Uncovered: 102,349,290 out of 103,014,375
Covered: 665,085 out of 103,014,375

Uncovered: 47,569,846 out of 48,193,658
Matches: 395,104 out of 48,193,658
Mismatches: 228,648 out of 48,193,658
Insertions: 60 out of 48,193,658

Phytophthora infestans T30-4

Uncovered: 228,074,831 out of 228,543,505
Covered: 468,674 out of 228,543,505

Uncovered: 21,984,694 out of 22,421,425
Matches: 274,537 out of 22,421,425
Mismatches: 162,143 out of 22,421,425
Insertions: 51 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

Tetrahymena thermophila 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}