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Hyaloperonospora arabidopsidis vs Guillardia theta CCMP2712 LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Hyaloperonospora arabidopsidis 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

ParameterHyaloperonospora arabidopsidisGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,657 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Hyaloperonospora arabidopsidis

Uncovered: 77,501,737 out of 78,897,814
Covered: 1,396,077 out of 78,897,814

Uncovered: 11,977,326 out of 13,171,834
Matches: 731,403 out of 13,171,834
Mismatches: 419,415 out of 13,171,834
Insertions: 43,690 out of 13,171,834
Identity over aligned base-pairs: 61.2%

Guillardia theta CCMP2712

Uncovered: 85,766,895 out of 87,266,873
Covered: 1,499,978 out of 87,266,873

Uncovered: 29,309,008 out of 30,644,092
Matches: 811,787 out of 30,644,092
Mismatches: 468,192 out of 30,644,092
Insertions: 55,105 out of 30,644,092
Identity over aligned base-pairs: 60.8%

Block size distribution

Size range All 5,657 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
21
123.0 bp
10 bp - 100 bp
1,367
95.0 kb
291
21.3 kb
100 bp - 1 kb
3,921
1.3 Mb
1,913
809.8 kb
1 kb - 10 kb
347
505.0 kb
645
1.1 Mb
10 kb - 100 kb
1
15.3 kb
1
15.3 kb