Tetrahymena thermophila vs Albugo laibachii Translated Blat results

Tetrahymena thermophila (Tetrahymena thermophila, JCVI-TTA1-2.2) 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 70. Tetrahymena thermophila 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

ParameterTetrahymena thermophilaAlbugo 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 5,410 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Tetrahymena thermophila

Uncovered: 102,364,433 out of 103,014,375
Covered: 649,942 out of 103,014,375

Uncovered: 47,579,273 out of 48,193,658
Matches: 400,414 out of 48,193,658
Mismatches: 213,887 out of 48,193,658
Insertions: 84 out of 48,193,658
Identity over aligned base-pairs: 65.2%

Albugo laibachii

Uncovered: 32,343,161 out of 32,766,811
Covered: 423,650 out of 32,766,811

Uncovered: 15,499,917 out of 15,902,867
Matches: 260,455 out of 15,902,867
Mismatches: 142,449 out of 15,902,867
Insertions: 46 out of 15,902,867
Identity over aligned base-pairs: 64.6%