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Hyaloperonospora arabidopsidis vs Pythium iwayamai LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 34,608 alignment blocks

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

Uncovered: 63,336,572 out of 78,897,814
Covered: 15,561,242 out of 78,897,814

Uncovered: 4,477,824 out of 13,171,834
Matches: 5,648,539 out of 13,171,834
Mismatches: 2,780,953 out of 13,171,834
Insertions: 264,518 out of 13,171,834
Identity over aligned base-pairs: 65.0%

Pythium iwayamai

Uncovered: 31,018,277 out of 43,199,174
Covered: 12,180,897 out of 43,199,174

Uncovered: 10,069,714 out of 19,552,457
Matches: 6,063,736 out of 19,552,457
Mismatches: 3,091,863 out of 19,552,457
Insertions: 327,144 out of 19,552,457
Identity over aligned base-pairs: 63.9%

Block size distribution

Size range All 34,608 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
136
787.0 bp
10 bp - 100 bp
4,341
283.8 kb
1,569
101.3 kb
100 bp - 1 kb
25,321
10.1 Mb
10,463
4.6 Mb
1 kb - 10 kb
4,799
7.9 Mb
5,716
12.9 Mb
10 kb - 100 kb
11
142.3 kb
70
892.7 kb