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Pythium ultimum vs Hyaloperonospora arabidopsidis LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Pythium ultimum 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

ParameterPythium ultimumHyaloperonospora arabidopsidis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 39,791 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium ultimum

Uncovered: 27,793,231 out of 44,913,582
Covered: 17,120,351 out of 44,913,582

Uncovered: 8,594,882 out of 19,826,256
Matches: 6,830,275 out of 19,826,256
Mismatches: 4,053,141 out of 19,826,256
Insertions: 347,958 out of 19,826,256
Identity over aligned base-pairs: 60.8%

Hyaloperonospora arabidopsidis

Uncovered: 50,691,540 out of 78,897,814
Covered: 28,206,274 out of 78,897,814

Uncovered: 3,339,520 out of 13,171,834
Matches: 6,003,385 out of 13,171,834
Mismatches: 3,525,948 out of 13,171,834
Insertions: 302,981 out of 13,171,834
Identity over aligned base-pairs: 61.1%

Block size distribution

Size range All 39,791 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
216
1.1 kb
10 bp - 100 bp
4,454
289.7 kb
1,179
80.3 kb
100 bp - 1 kb
26,288
10.8 Mb
9,471
4.2 Mb
1 kb - 10 kb
8,501
18.3 Mb
7,014
20.5 Mb
10 kb - 100 kb
332
5.6 Mb
573
10.0 Mb
100 kb - 1 Mb
2
213.1 kb