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Pythium arrhenomanes vs Pythium vexans LastZ results

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) and Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_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 arrhenomanesPythium vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 34,982 alignment blocks

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

Uncovered: 25,425,026 out of 44,672,625
Covered: 19,247,599 out of 44,672,625

Uncovered: 4,240,315 out of 18,367,184
Matches: 9,302,740 out of 18,367,184
Mismatches: 4,215,888 out of 18,367,184
Insertions: 608,241 out of 18,367,184
Identity over aligned base-pairs: 65.9%

Pythium vexans

Uncovered: 14,997,773 out of 33,844,883
Covered: 18,847,110 out of 33,844,883

Uncovered: 3,870,398 out of 18,608,353
Matches: 9,590,321 out of 18,608,353
Mismatches: 4,542,264 out of 18,608,353
Insertions: 605,370 out of 18,608,353
Identity over aligned base-pairs: 65.1%

Block size distribution

Size range All 34,982 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
117
688.0 bp
10 bp - 100 bp
3,568
238.3 kb
1,039
72.9 kb
100 bp - 1 kb
24,128
10.2 Mb
8,934
4.0 Mb
1 kb - 10 kb
7,154
12.6 Mb
6,187
16.1 Mb
10 kb - 100 kb
15
186.8 kb
207
3.0 Mb