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Pythium arrhenomanes vs Phytophthora parasitica LastZ results

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium arrhenomanes 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

ParameterPythium arrhenomanesPhytophthora parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 43,786 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium arrhenomanes

Uncovered: 26,717,311 out of 44,672,625
Covered: 17,955,314 out of 44,672,625

Uncovered: 4,940,563 out of 18,367,184
Matches: 8,583,291 out of 18,367,184
Mismatches: 4,292,032 out of 18,367,184
Insertions: 551,298 out of 18,367,184
Identity over aligned base-pairs: 63.9%

Phytophthora parasitica

Uncovered: 33,543,721 out of 55,229,644
Covered: 21,685,923 out of 55,229,644

Uncovered: 10,600,197 out of 27,601,672
Matches: 10,672,740 out of 27,601,672
Mismatches: 5,744,614 out of 27,601,672
Insertions: 584,121 out of 27,601,672
Identity over aligned base-pairs: 62.8%

Block size distribution

Size range All 43,786 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
133
709.0 bp
10 bp - 100 bp
4,514
305.6 kb
1,159
83.6 kb
100 bp - 1 kb
31,655
13.0 Mb
12,555
5.7 Mb
1 kb - 10 kb
7,471
12.5 Mb
7,766
18.4 Mb
10 kb - 100 kb
13
174.8 kb
125
1.7 Mb