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Phaeodactylum tricornutum vs Phytophthora parasitica LastZ results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phaeodactylum tricornutum 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

ParameterPhaeodactylum tricornutumPhytophthora parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,984 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phaeodactylum tricornutum

Uncovered: 25,611,792 out of 27,568,093
Covered: 1,956,301 out of 27,568,093

Uncovered: 15,978,568 out of 17,873,974
Matches: 1,136,594 out of 17,873,974
Mismatches: 676,079 out of 17,873,974
Insertions: 82,733 out of 17,873,974
Identity over aligned base-pairs: 60.0%

Phytophthora parasitica

Uncovered: 52,934,704 out of 55,229,644
Covered: 2,294,940 out of 55,229,644

Uncovered: 25,388,116 out of 27,601,672
Matches: 1,331,293 out of 27,601,672
Mismatches: 802,049 out of 27,601,672
Insertions: 80,214 out of 27,601,672
Identity over aligned base-pairs: 60.1%

Block size distribution

Size range All 5,984 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
21
113.0 bp
10 bp - 100 bp
713
49.9 kb
187
13.4 kb
100 bp - 1 kb
4,647
1.8 Mb
2,251
1.1 Mb
1 kb - 10 kb
603
877.0 kb
987
1.6 Mb