In this section

Phytophthora ramorum vs Hyaloperonospora arabidopsidis LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phytophthora ramorum 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

ParameterPhytophthora ramorumHyaloperonospora arabidopsidis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 38,688 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora ramorum

Uncovered: 42,055,502 out of 66,652,401
Covered: 24,596,899 out of 66,652,401

Uncovered: 7,571,743 out of 22,377,278
Matches: 10,036,880 out of 22,377,278
Mismatches: 4,500,301 out of 22,377,278
Insertions: 268,354 out of 22,377,278
Identity over aligned base-pairs: 67.8%

Hyaloperonospora arabidopsidis

Uncovered: 49,548,079 out of 78,897,814
Covered: 29,349,735 out of 78,897,814

Uncovered: 1,748,014 out of 13,171,834
Matches: 7,894,944 out of 13,171,834
Mismatches: 3,276,785 out of 13,171,834
Insertions: 252,091 out of 13,171,834
Identity over aligned base-pairs: 69.1%

Block size distribution

Size range All 38,688 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
223
1.2 kb
10 bp - 100 bp
3,646
235.9 kb
1,259
88.5 kb
100 bp - 1 kb
23,388
10.2 Mb
11,143
5.2 Mb
1 kb - 10 kb
11,242
25.5 Mb
7,488
20.0 Mb
10 kb - 100 kb
189
3.4 Mb
562
13.2 Mb
100 kb - 1 Mb
7
935.8 kb