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Hyaloperonospora arabidopsidis vs Pythium arrhenomanes LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_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 arrhenomanes
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 30,263 alignment blocks

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

Uncovered: 64,630,006 out of 78,897,814
Covered: 14,267,808 out of 78,897,814

Uncovered: 4,811,017 out of 13,171,834
Matches: 5,321,888 out of 13,171,834
Mismatches: 2,747,745 out of 13,171,834
Insertions: 291,184 out of 13,171,834
Identity over aligned base-pairs: 63.7%

Pythium arrhenomanes

Uncovered: 33,267,342 out of 44,672,625
Covered: 11,405,283 out of 44,672,625

Uncovered: 9,570,092 out of 18,367,184
Matches: 5,563,634 out of 18,367,184
Mismatches: 2,927,589 out of 18,367,184
Insertions: 305,869 out of 18,367,184
Identity over aligned base-pairs: 63.2%

Block size distribution

Size range All 30,263 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
83
464.0 bp
10 bp - 100 bp
3,212
219.9 kb
852
61.3 kb
100 bp - 1 kb
22,245
9.1 Mb
8,820
4.2 Mb
1 kb - 10 kb
4,719
7.7 Mb
5,415
12.2 Mb
10 kb - 100 kb
4
65.5 kb
39
555.1 kb