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Hyaloperonospora arabidopsidis vs Albugo laibachii LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Albugo laibachii (Albugo laibachii, ENA1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. 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 arabidopsidisAlbugo laibachii
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 34,843 alignment blocks

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

Uncovered: 60,675,894 out of 78,897,814
Covered: 18,221,920 out of 78,897,814

Uncovered: 7,295,087 out of 13,171,834
Matches: 3,629,089 out of 13,171,834
Mismatches: 2,042,673 out of 13,171,834
Insertions: 204,985 out of 13,171,834
Identity over aligned base-pairs: 61.8%

Albugo laibachii

Uncovered: 20,203,510 out of 32,766,811
Covered: 12,563,301 out of 32,766,811

Uncovered: 8,320,651 out of 15,902,867
Matches: 4,242,163 out of 15,902,867
Mismatches: 3,133,280 out of 15,902,867
Insertions: 206,773 out of 15,902,867
Identity over aligned base-pairs: 55.9%

Block size distribution

Size range All 34,843 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
197
968.0 bp
10 bp - 100 bp
5,050
338.4 kb
2,257
155.5 kb
100 bp - 1 kb
22,468
9.0 Mb
9,628
4.2 Mb
1 kb - 10 kb
7,061
14.5 Mb
7,325
18.8 Mb
10 kb - 100 kb
67
1.3 Mb
91
1.7 Mb
100 kb - 1 Mb
1
109.5 kb