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Albugo laibachii vs Phytophthora lateralis LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Albugo laibachii 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

ParameterAlbugo laibachiiPhytophthora lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 23,167 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Albugo laibachii

Uncovered: 22,608,023 out of 32,766,811
Covered: 10,158,788 out of 32,766,811

Uncovered: 8,619,289 out of 15,902,867
Matches: 4,431,844 out of 15,902,867
Mismatches: 2,617,641 out of 15,902,867
Insertions: 234,093 out of 15,902,867
Identity over aligned base-pairs: 60.8%

Phytophthora lateralis

Uncovered: 34,834,844 out of 43,981,379
Covered: 9,146,535 out of 43,981,379

Uncovered: 8,269,724 out of 14,242,768
Matches: 3,655,345 out of 14,242,768
Mismatches: 2,130,473 out of 14,242,768
Insertions: 187,226 out of 14,242,768
Identity over aligned base-pairs: 61.2%

Block size distribution

Size range All 23,167 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
75
378.0 bp
10 bp - 100 bp
2,247
155.8 kb
588
42.0 kb
100 bp - 1 kb
17,095
7.1 Mb
6,957
3.2 Mb
1 kb - 10 kb
3,743
6.1 Mb
4,521
9.8 Mb
10 kb - 100 kb
7
80.2 kb
30
415.1 kb