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Phytophthora parasitica vs Guillardia theta CCMP2712 LastZ results

Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phytophthora parasitica 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

ParameterPhytophthora parasiticaGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,416 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora parasitica

Uncovered: 52,953,279 out of 55,229,644
Covered: 2,276,365 out of 55,229,644

Uncovered: 25,425,733 out of 27,601,672
Matches: 1,320,306 out of 27,601,672
Mismatches: 767,465 out of 27,601,672
Insertions: 88,168 out of 27,601,672
Identity over aligned base-pairs: 60.7%

Guillardia theta CCMP2712

Uncovered: 85,018,920 out of 87,266,873
Covered: 2,247,953 out of 87,266,873

Uncovered: 28,654,051 out of 30,644,092
Matches: 1,212,479 out of 30,644,092
Mismatches: 691,521 out of 30,644,092
Insertions: 86,041 out of 30,644,092
Identity over aligned base-pairs: 60.9%

Block size distribution

Size range All 8,416 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
38
175.0 bp
10 bp - 100 bp
1,951
135.8 kb
465
33.5 kb
100 bp - 1 kb
5,777
2.0 Mb
2,870
1.2 Mb
1 kb - 10 kb
650
1.0 Mb
956
1.8 Mb
10 kb - 100 kb
11
137.8 kb