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Hyaloperonospora arabidopsidis vs Phytophthora parasitica LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_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 arabidopsidisPhytophthora parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 47,257 alignment blocks

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

Uncovered: 47,082,045 out of 78,897,814
Covered: 31,815,769 out of 78,897,814

Uncovered: 1,646,696 out of 13,171,834
Matches: 8,258,201 out of 13,171,834
Mismatches: 2,972,286 out of 13,171,834
Insertions: 294,651 out of 13,171,834
Identity over aligned base-pairs: 71.7%

Phytophthora parasitica

Uncovered: 34,197,160 out of 55,229,644
Covered: 21,032,484 out of 55,229,644

Uncovered: 11,974,186 out of 27,601,672
Matches: 10,500,507 out of 27,601,672
Mismatches: 4,846,528 out of 27,601,672
Insertions: 280,451 out of 27,601,672
Identity over aligned base-pairs: 67.2%

Block size distribution

Size range All 47,257 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
342
1.6 kb
10 bp - 100 bp
5,379
340.0 kb
1,798
129.8 kb
100 bp - 1 kb
28,889
11.7 Mb
14,676
6.1 Mb
1 kb - 10 kb
12,592
26.5 Mb
8,841
24.9 Mb
10 kb - 100 kb
55
791.4 kb
456
8.2 Mb