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Albugo laibachii vs Guillardia theta CCMP2712 LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) 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 laibachiiGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,163 alignment blocks

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

Uncovered: 31,369,186 out of 32,766,811
Covered: 1,397,625 out of 32,766,811

Uncovered: 14,609,963 out of 15,902,867
Matches: 771,552 out of 15,902,867
Mismatches: 473,348 out of 15,902,867
Insertions: 48,004 out of 15,902,867
Identity over aligned base-pairs: 59.7%

Guillardia theta CCMP2712

Uncovered: 85,756,943 out of 87,266,873
Covered: 1,509,930 out of 87,266,873

Uncovered: 29,271,987 out of 30,644,092
Matches: 820,638 out of 30,644,092
Mismatches: 499,141 out of 30,644,092
Insertions: 52,326 out of 30,644,092
Identity over aligned base-pairs: 59.8%

Block size distribution

Size range All 5,163 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
13
63.0 bp
10 bp - 100 bp
1,134
78.6 kb
214
15.9 kb
100 bp - 1 kb
3,607
1.2 Mb
1,700
738.7 kb
1 kb - 10 kb
409
663.1 kb
603
1.1 Mb
10 kb - 100 kb
8
100.1 kb