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Phaeodactylum tricornutum vs Phytophthora kernoviae LastZ results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) and Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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 kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,936 alignment blocks

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

Uncovered: 25,588,838 out of 27,568,093
Covered: 1,979,255 out of 27,568,093

Uncovered: 15,985,803 out of 17,873,974
Matches: 1,129,032 out of 17,873,974
Mismatches: 676,454 out of 17,873,974
Insertions: 82,685 out of 17,873,974
Identity over aligned base-pairs: 59.8%

Phytophthora kernoviae

Uncovered: 40,936,186 out of 43,208,681
Covered: 2,272,495 out of 43,208,681

Uncovered: 9,689,591 out of 11,344,308
Matches: 1,001,097 out of 11,344,308
Mismatches: 597,196 out of 11,344,308
Insertions: 56,424 out of 11,344,308
Identity over aligned base-pairs: 60.5%

Block size distribution

Size range All 5,936 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
12
51.0 bp
10 bp - 100 bp
761
53.6 kb
191
13.4 kb
100 bp - 1 kb
4,550
1.7 Mb
2,243
1.1 Mb
1 kb - 10 kb
613
901.5 kb
980
1.6 Mb
10 kb - 100 kb
2
25.1 kb