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Pythium arrhenomanes vs Phytophthora lateralis LastZ results

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium arrhenomanes 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

ParameterPythium arrhenomanesPhytophthora lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 39,190 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium arrhenomanes

Uncovered: 28,614,671 out of 44,672,625
Covered: 16,057,954 out of 44,672,625

Uncovered: 6,496,042 out of 18,367,184
Matches: 7,625,683 out of 18,367,184
Mismatches: 3,742,133 out of 18,367,184
Insertions: 503,326 out of 18,367,184
Identity over aligned base-pairs: 64.2%

Phytophthora lateralis

Uncovered: 26,062,590 out of 43,981,379
Covered: 17,918,789 out of 43,981,379

Uncovered: 3,935,574 out of 14,242,768
Matches: 6,645,740 out of 14,242,768
Mismatches: 3,303,834 out of 14,242,768
Insertions: 357,620 out of 14,242,768
Identity over aligned base-pairs: 64.5%

Block size distribution

Size range All 39,190 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
135
711.0 bp
10 bp - 100 bp
4,163
283.0 kb
1,257
90.5 kb
100 bp - 1 kb
28,639
11.5 Mb
12,272
5.4 Mb
1 kb - 10 kb
6,239
10.4 Mb
6,502
15.2 Mb
10 kb - 100 kb
14
170.0 kb
118
1.7 Mb