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Albugo laibachii vs Pythium vexans LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) 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 laibachiiPythium vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 19,732 alignment blocks

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

Uncovered: 22,668,152 out of 32,766,811
Covered: 10,098,659 out of 32,766,811

Uncovered: 7,829,074 out of 15,902,867
Matches: 4,937,407 out of 15,902,867
Mismatches: 2,909,049 out of 15,902,867
Insertions: 227,337 out of 15,902,867
Identity over aligned base-pairs: 61.2%

Pythium vexans

Uncovered: 24,911,779 out of 33,844,883
Covered: 8,933,104 out of 33,844,883

Uncovered: 11,081,914 out of 18,608,353
Matches: 4,577,322 out of 18,608,353
Mismatches: 2,695,537 out of 18,608,353
Insertions: 253,580 out of 18,608,353
Identity over aligned base-pairs: 60.8%

Block size distribution

Size range All 19,732 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
20
81.0 bp
10 bp - 100 bp
1,825
127.7 kb
309
22.3 kb
100 bp - 1 kb
14,452
6.1 Mb
5,123
2.6 Mb
1 kb - 10 kb
3,425
5.6 Mb
3,996
8.8 Mb
10 kb - 100 kb
10
124.1 kb
43
578.7 kb