Paramecium tetraurelia vs Phaeodactylum tricornutum Translated Blat results

Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) and Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) 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

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

ParameterParamecium tetraureliaPhaeodactylum tricornutum
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 6,516 alignment blocks

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

Uncovered: 71,168,611 out of 72,094,543
Covered: 925,932 out of 72,094,543

Uncovered: 53,140,934 out of 54,045,570
Matches: 573,210 out of 54,045,570
Mismatches: 330,875 out of 54,045,570
Insertions: 551 out of 54,045,570
Identity over aligned base-pairs: 63.4%

Phaeodactylum tricornutum

Uncovered: 27,244,314 out of 27,568,093
Covered: 323,779 out of 27,568,093

Uncovered: 14,098,726 out of 14,407,044
Matches: 193,333 out of 14,407,044
Mismatches: 114,917 out of 14,407,044
Insertions: 68 out of 14,407,044
Identity over aligned base-pairs: 62.7%