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Phaeodactylum tricornutum vs Pythium vexans LastZ results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) and Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phaeodactylum tricornutum was used as the reference species. After running LastZ, the raw LastZ 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
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterPhaeodactylum tricornutumPythium vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,765 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phaeodactylum tricornutum

Uncovered: 25,681,617 out of 27,568,093
Covered: 1,886,476 out of 27,568,093

Uncovered: 16,040,281 out of 17,873,974
Matches: 1,101,180 out of 17,873,974
Mismatches: 654,094 out of 17,873,974
Insertions: 78,419 out of 17,873,974
Identity over aligned base-pairs: 60.1%

Pythium vexans

Uncovered: 31,766,668 out of 33,844,883
Covered: 2,078,215 out of 33,844,883

Uncovered: 16,724,822 out of 18,608,353
Matches: 1,135,837 out of 18,608,353
Mismatches: 677,093 out of 18,608,353
Insertions: 70,601 out of 18,608,353
Identity over aligned base-pairs: 60.3%

Block size distribution

Size range All 5,765 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
12
56.0 bp
10 bp - 100 bp
838
59.3 kb
185
13.2 kb
100 bp - 1 kb
4,357
1.6 Mb
2,067
980.5 kb
1 kb - 10 kb
558
814.2 kb
894
1.5 Mb
10 kb - 100 kb
1
10.5 kb