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Hyaloperonospora arabidopsidis vs Pythium vexans LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Hyaloperonospora arabidopsidis 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

ParameterHyaloperonospora arabidopsidisPythium vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 31,667 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Hyaloperonospora arabidopsidis

Uncovered: 60,979,676 out of 78,897,814
Covered: 17,918,138 out of 78,897,814

Uncovered: 3,600,229 out of 13,171,834
Matches: 6,268,955 out of 13,171,834
Mismatches: 2,977,769 out of 13,171,834
Insertions: 324,881 out of 13,171,834
Identity over aligned base-pairs: 65.5%

Pythium vexans

Uncovered: 20,594,190 out of 33,844,883
Covered: 13,250,693 out of 33,844,883

Uncovered: 8,045,084 out of 18,608,353
Matches: 6,728,082 out of 18,608,353
Mismatches: 3,505,177 out of 18,608,353
Insertions: 330,010 out of 18,608,353
Identity over aligned base-pairs: 63.7%

Block size distribution

Size range All 31,667 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
91
505.0 bp
10 bp - 100 bp
3,285
218.6 kb
960
61.8 kb
100 bp - 1 kb
21,925
9.3 Mb
8,157
3.9 Mb
1 kb - 10 kb
6,346
11.1 Mb
5,882
14.8 Mb
10 kb - 100 kb
20
299.7 kb
151
2.2 Mb