Guillardia theta CCMP2712 vs Hyaloperonospora arabidopsidis Translated Blat results

Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) and Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 76. Guillardia theta CCMP2712 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

ParameterGuillardia theta CCMP2712Hyaloperonospora arabidopsidis
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 6,778 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Guillardia theta CCMP2712

Uncovered: 86,465,499 out of 87,266,873
Covered: 801,374 out of 87,266,873

Uncovered: 29,875,962 out of 30,644,092
Matches: 514,724 out of 30,644,092
Mismatches: 252,789 out of 30,644,092
Insertions: 617 out of 30,644,092
Identity over aligned base-pairs: 67.0%

Hyaloperonospora arabidopsidis

Uncovered: 78,281,299 out of 78,897,814
Covered: 616,515 out of 78,897,814

Uncovered: 12,604,495 out of 13,171,834
Matches: 378,853 out of 13,171,834
Mismatches: 188,383 out of 13,171,834
Insertions: 103 out of 13,171,834
Identity over aligned base-pairs: 66.8%