Paramecium tetraurelia vs Albugo laibachii Translated Blat results

Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) and Albugo laibachii (Albugo laibachii, ENA1) 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 tetraureliaAlbugo laibachii
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 10,337 alignment blocks

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

Uncovered: 70,744,203 out of 72,094,543
Covered: 1,350,340 out of 72,094,543

Uncovered: 52,726,793 out of 54,045,570
Matches: 857,320 out of 54,045,570
Mismatches: 460,743 out of 54,045,570
Insertions: 714 out of 54,045,570
Identity over aligned base-pairs: 65.0%

Albugo laibachii

Uncovered: 32,269,590 out of 32,766,811
Covered: 497,221 out of 32,766,811

Uncovered: 15,429,235 out of 15,902,867
Matches: 303,562 out of 15,902,867
Mismatches: 169,968 out of 15,902,867
Insertions: 102 out of 15,902,867
Identity over aligned base-pairs: 64.1%