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Albugo laibachii vs Pythium arrhenomanes LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_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 arrhenomanes
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 20,797 alignment blocks

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

Uncovered: 23,073,866 out of 32,766,811
Covered: 9,692,945 out of 32,766,811

Uncovered: 8,056,598 out of 15,902,867
Matches: 4,760,329 out of 15,902,867
Mismatches: 2,860,227 out of 15,902,867
Insertions: 225,713 out of 15,902,867
Identity over aligned base-pairs: 60.7%

Pythium arrhenomanes

Uncovered: 36,161,786 out of 44,672,625
Covered: 8,510,839 out of 44,672,625

Uncovered: 11,475,444 out of 18,367,184
Matches: 4,212,555 out of 18,367,184
Mismatches: 2,449,816 out of 18,367,184
Insertions: 229,369 out of 18,367,184
Identity over aligned base-pairs: 61.1%

Block size distribution

Size range All 20,797 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
31
176.0 bp
10 bp - 100 bp
2,217
155.7 kb
383
28.2 kb
100 bp - 1 kb
15,491
6.4 Mb
5,882
2.9 Mb
1 kb - 10 kb
3,054
4.9 Mb
4,027
8.2 Mb
10 kb - 100 kb
4
46.0 kb
22
304.5 kb