Paramecium tetraurelia vs Tetrahymena thermophila Translated Blat results

Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) and Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) 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 tetraureliaTetrahymena thermophila
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 48,364 alignment blocks

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

Uncovered: 66,818,399 out of 72,094,543
Covered: 5,276,144 out of 72,094,543

Uncovered: 48,984,303 out of 54,045,570
Matches: 3,501,266 out of 54,045,570
Mismatches: 1,557,057 out of 54,045,570
Insertions: 2,944 out of 54,045,570
Identity over aligned base-pairs: 69.2%

Tetrahymena thermophila

Uncovered: 100,610,725 out of 103,014,375
Covered: 2,403,650 out of 103,014,375

Uncovered: 46,012,809 out of 48,193,658
Matches: 1,498,886 out of 48,193,658
Mismatches: 681,526 out of 48,193,658
Insertions: 437 out of 48,193,658
Identity over aligned base-pairs: 68.7%