In this section

Hyaloperonospora arabidopsidis vs Pythium aphanidermatum LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_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 aphanidermatum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 31,878 alignment blocks

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

Uncovered: 60,274,416 out of 78,897,814
Covered: 18,623,398 out of 78,897,814

Uncovered: 4,560,121 out of 13,171,834
Matches: 5,466,582 out of 13,171,834
Mismatches: 2,815,422 out of 13,171,834
Insertions: 329,709 out of 13,171,834
Identity over aligned base-pairs: 63.5%

Pythium aphanidermatum

Uncovered: 24,342,468 out of 35,876,849
Covered: 11,534,381 out of 35,876,849

Uncovered: 8,789,065 out of 18,015,574
Matches: 5,791,774 out of 18,015,574
Mismatches: 3,155,041 out of 18,015,574
Insertions: 279,694 out of 18,015,574
Identity over aligned base-pairs: 62.8%

Block size distribution

Size range All 31,878 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
119
552.0 bp
10 bp - 100 bp
3,045
206.6 kb
658
45.7 kb
100 bp - 1 kb
22,228
9.5 Mb
8,021
3.8 Mb
1 kb - 10 kb
6,461
11.2 Mb
5,832
15.5 Mb
10 kb - 100 kb
25
387.0 kb
128
1.9 Mb