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Hyaloperonospora arabidopsidis vs Phytophthora lateralis LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) 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 arabidopsidisPhytophthora lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 52,942 alignment blocks

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

Uncovered: 49,208,675 out of 78,897,814
Covered: 29,689,139 out of 78,897,814

Uncovered: 3,431,591 out of 13,171,834
Matches: 6,929,891 out of 13,171,834
Mismatches: 2,569,079 out of 13,171,834
Insertions: 241,273 out of 13,171,834
Identity over aligned base-pairs: 71.1%

Phytophthora lateralis

Uncovered: 26,057,755 out of 43,981,379
Covered: 17,923,624 out of 43,981,379

Uncovered: 4,302,988 out of 14,242,768
Matches: 6,751,435 out of 14,242,768
Mismatches: 3,007,611 out of 14,242,768
Insertions: 180,734 out of 14,242,768
Identity over aligned base-pairs: 67.9%

Block size distribution

Size range All 52,942 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
461
2.3 kb
10 bp - 100 bp
6,207
389.4 kb
2,034
146.2 kb
100 bp - 1 kb
35,510
14.0 Mb
17,290
6.9 Mb
1 kb - 10 kb
10,705
21.3 Mb
8,837
23.5 Mb
10 kb - 100 kb
59
885.4 kb
353
6.0 Mb