Phytophthora lateralis vs Paramecium tetraurelia Translated Blat results

Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) and Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 76. Phytophthora lateralis was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

ParameterPhytophthora lateralisParamecium tetraurelia
Chunk size1,000,0001,000,000
Overlap10,00010,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 2,684 alignment blocks

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

Uncovered: 43,596,432 out of 43,981,379
Covered: 384,947 out of 43,981,379

Uncovered: 14,327,443 out of 14,663,433
Matches: 206,438 out of 14,663,433
Mismatches: 129,522 out of 14,663,433
Insertions: 30 out of 14,663,433
Identity over aligned base-pairs: 61.4%

Paramecium tetraurelia

Uncovered: 71,759,292 out of 72,094,543
Covered: 335,251 out of 72,094,543

Uncovered: 53,715,017 out of 54,045,570
Matches: 203,113 out of 54,045,570
Mismatches: 127,302 out of 54,045,570
Insertions: 138 out of 54,045,570
Identity over aligned base-pairs: 61.4%