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Albugo laibachii vs Phytophthora parasitica LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_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 laibachiiPhytophthora parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 25,546 alignment blocks

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

Uncovered: 21,107,419 out of 32,766,811
Covered: 11,659,392 out of 32,766,811

Uncovered: 7,220,022 out of 15,902,867
Matches: 5,328,699 out of 15,902,867
Mismatches: 3,068,503 out of 15,902,867
Insertions: 285,643 out of 15,902,867
Identity over aligned base-pairs: 61.4%

Phytophthora parasitica

Uncovered: 43,662,894 out of 55,229,644
Covered: 11,566,750 out of 55,229,644

Uncovered: 18,228,064 out of 27,601,672
Matches: 5,718,174 out of 27,601,672
Mismatches: 3,335,586 out of 27,601,672
Insertions: 319,848 out of 27,601,672
Identity over aligned base-pairs: 61.0%

Block size distribution

Size range All 25,546 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
66
326.0 bp
10 bp - 100 bp
2,441
169.1 kb
578
41.8 kb
100 bp - 1 kb
18,269
7.8 Mb
6,953
3.5 Mb
1 kb - 10 kb
4,765
8.0 Mb
5,428
11.9 Mb
10 kb - 100 kb
5
60.0 kb
35
491.7 kb