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Albugo laibachii vs Bigelowiella natans LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. 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 laibachiiBigelowiella natans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,499 alignment blocks

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

Uncovered: 31,596,930 out of 32,766,811
Covered: 1,169,881 out of 32,766,811

Uncovered: 14,833,265 out of 15,902,867
Matches: 648,030 out of 15,902,867
Mismatches: 385,512 out of 15,902,867
Insertions: 36,060 out of 15,902,867
Identity over aligned base-pairs: 60.6%

Bigelowiella natans

Uncovered: 93,552,319 out of 94,701,163
Covered: 1,148,844 out of 94,701,163

Uncovered: 27,781,885 out of 28,817,508
Matches: 638,463 out of 28,817,508
Mismatches: 365,888 out of 28,817,508
Insertions: 31,272 out of 28,817,508
Identity over aligned base-pairs: 61.7%

Block size distribution

Size range All 5,499 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
31
169.0 bp
10 bp - 100 bp
1,766
122.4 kb
361
25.6 kb
100 bp - 1 kb
3,455
973.6 kb
1,734
688.0 kb
1 kb - 10 kb
247
419.5 kb
404
769.0 kb
10 kb - 100 kb
3
33.0 kb