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Pythium ultimum vs Albugo laibachii LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Albugo laibachii (Albugo laibachii, ENA1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Pythium ultimum 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

ParameterPythium ultimumAlbugo laibachii
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 24,369 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium ultimum

Uncovered: 33,246,786 out of 44,913,582
Covered: 11,666,796 out of 44,913,582

Uncovered: 11,446,611 out of 19,826,256
Matches: 5,149,608 out of 19,826,256
Mismatches: 2,948,173 out of 19,826,256
Insertions: 281,864 out of 19,826,256
Identity over aligned base-pairs: 61.5%

Albugo laibachii

Uncovered: 20,962,647 out of 32,766,811
Covered: 11,804,164 out of 32,766,811

Uncovered: 7,114,070 out of 15,902,867
Matches: 5,296,181 out of 15,902,867
Mismatches: 3,243,520 out of 15,902,867
Insertions: 249,096 out of 15,902,867
Identity over aligned base-pairs: 60.3%

Block size distribution

Size range All 24,369 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
83
303.0 bp
10 bp - 100 bp
2,731
188.8 kb
750
54.1 kb
100 bp - 1 kb
16,749
7.1 Mb
6,257
3.0 Mb
1 kb - 10 kb
4,781
8.2 Mb
4,993
11.4 Mb
10 kb - 100 kb
25
343.9 kb
85
1.3 Mb