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Hyaloperonospora arabidopsidis vs Bigelowiella natans LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) 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 arabidopsidisBigelowiella natans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,680 alignment blocks

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

Uncovered: 77,789,983 out of 78,897,814
Covered: 1,107,831 out of 78,897,814

Uncovered: 12,249,825 out of 13,171,834
Matches: 567,897 out of 13,171,834
Mismatches: 326,190 out of 13,171,834
Insertions: 27,922 out of 13,171,834
Identity over aligned base-pairs: 61.6%

Bigelowiella natans

Uncovered: 93,553,676 out of 94,701,163
Covered: 1,147,487 out of 94,701,163

Uncovered: 27,811,069 out of 28,817,508
Matches: 612,827 out of 28,817,508
Mismatches: 367,595 out of 28,817,508
Insertions: 26,017 out of 28,817,508
Identity over aligned base-pairs: 60.9%

Block size distribution

Size range All 5,680 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
25
101.0 bp
10 bp - 100 bp
1,941
136.0 kb
408
28.6 kb
100 bp - 1 kb
3,494
955.1 kb
1,728
685.3 kb
1 kb - 10 kb
218
324.5 kb
426
701.8 kb
10 kb - 100 kb
2
47.3 kb
2
47.3 kb