Leishmania major vs Hyaloperonospora arabidopsidis Translated Blat Results

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Leishmania major (Leishmania major strain Friedlin, ASM272v2) 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 74. Leishmania major was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.


Number of alignment blocks: 3,510

Genome coverage (bp) Coding exon coverage (bp)
Leishmania major strain Friedlin

Uncovered: 32,310,958 out of 32,855,095
Covered: 544,137 out of 32,855,095

Uncovered: 15,189,192 out of 15,726,087
Matches: 365,896 out of 15,726,087
Mismatches: 170,925 out of 15,726,087
Insertions: 74 out of 15,726,087

Hyaloperonospora arabidopsidis

Uncovered: 78,537,767 out of 78,897,814
Covered: 360,047 out of 78,897,814

Uncovered: 12,836,523 out of 13,171,834
Matches: 223,545 out of 13,171,834
Mismatches: 111,739 out of 13,171,834
Insertions: 27 out of 13,171,834

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

Leishmania major Hyaloperonospora arabidopsidis
Chunk size 1,000,000 1,000,000
Overlap 10,000 10,000
Group set size 100,000,000 100,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}