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Hyaloperonospora arabidopsidis vs Phytophthora infestans LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) 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 infestans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 45,131 alignment blocks

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

Uncovered: 55,092,635 out of 78,897,814
Covered: 23,805,179 out of 78,897,814

Uncovered: 1,943,826 out of 13,171,834
Matches: 7,750,490 out of 13,171,834
Mismatches: 3,200,953 out of 13,171,834
Insertions: 276,565 out of 13,171,834
Identity over aligned base-pairs: 69.0%

Phytophthora infestans

Uncovered: 199,535,176 out of 228,543,505
Covered: 29,008,329 out of 228,543,505

Uncovered: 8,444,005 out of 22,421,425
Matches: 9,633,259 out of 22,421,425
Mismatches: 4,128,849 out of 22,421,425
Insertions: 215,312 out of 22,421,425
Identity over aligned base-pairs: 68.9%

Block size distribution

Size range All 45,131 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
333
1.9 kb
10 bp - 100 bp
5,518
355.9 kb
2,301
163.0 kb
100 bp - 1 kb
28,541
11.3 Mb
15,786
6.4 Mb
1 kb - 10 kb
10,521
22.7 Mb
7,542
19.3 Mb
10 kb - 100 kb
218
3.9 Mb
497
11.3 Mb
100 kb - 1 Mb
7
1.1 Mb