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Phytophthora kernoviae vs Phytophthora lateralis LastZ results

Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Phytophthora kernoviae 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 kernoviaePhytophthora lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 37,282 alignment blocks

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

Uncovered: 19,189,432 out of 43,208,681
Covered: 24,019,249 out of 43,208,681

Uncovered: 2,192,251 out of 11,344,308
Matches: 6,870,724 out of 11,344,308
Mismatches: 2,099,586 out of 11,344,308
Insertions: 181,747 out of 11,344,308
Identity over aligned base-pairs: 75.1%

Phytophthora lateralis

Uncovered: 17,760,505 out of 43,981,379
Covered: 26,220,874 out of 43,981,379

Uncovered: 1,314,534 out of 14,242,768
Matches: 9,558,897 out of 14,242,768
Mismatches: 3,177,005 out of 14,242,768
Insertions: 192,332 out of 14,242,768
Identity over aligned base-pairs: 73.9%

Block size distribution

Size range All 37,282 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
301
1.5 kb
10 bp - 100 bp
4,470
294.9 kb
1,929
139.4 kb
100 bp - 1 kb
23,733
9.3 Mb
12,424
4.9 Mb
1 kb - 10 kb
8,689
20.2 Mb
4,977
12.7 Mb
10 kb - 100 kb
89
1.2 Mb
632
13.2 Mb