Paramecium tetraurelia vs Pythium ultimum Translated Blat results

Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) and Pythium ultimum (Pythium ultimum DAOM BR144, pug) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 72. Paramecium tetraurelia 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

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

ParameterParamecium tetraureliaPythium ultimum
Chunk size1,000,0001,000,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 8,088 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Paramecium tetraurelia

Uncovered: 70,875,251 out of 72,094,543
Covered: 1,219,292 out of 72,094,543

Uncovered: 52,853,524 out of 54,045,570
Matches: 740,480 out of 54,045,570
Mismatches: 450,876 out of 54,045,570
Insertions: 690 out of 54,045,570
Identity over aligned base-pairs: 62.1%

Pythium ultimum

Uncovered: 44,442,150 out of 44,913,582
Covered: 471,432 out of 44,913,582

Uncovered: 19,408,857 out of 19,826,256
Matches: 256,286 out of 19,826,256
Mismatches: 161,056 out of 19,826,256
Insertions: 57 out of 19,826,256
Identity over aligned base-pairs: 61.4%