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Pythium ultimum vs Phytophthora lateralis LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium ultimum 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 ultimumPhytophthora lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 38,421 alignment blocks

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

Uncovered: 25,106,269 out of 44,913,582
Covered: 19,807,313 out of 44,913,582

Uncovered: 5,692,943 out of 19,826,256
Matches: 9,194,856 out of 19,826,256
Mismatches: 4,363,973 out of 19,826,256
Insertions: 574,484 out of 19,826,256
Identity over aligned base-pairs: 65.1%

Phytophthora lateralis

Uncovered: 24,249,552 out of 43,981,379
Covered: 19,731,827 out of 43,981,379

Uncovered: 3,070,211 out of 14,242,768
Matches: 7,330,008 out of 14,242,768
Mismatches: 3,509,624 out of 14,242,768
Insertions: 332,925 out of 14,242,768
Identity over aligned base-pairs: 65.6%

Block size distribution

Size range All 38,421 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
179
872.0 bp
10 bp - 100 bp
4,259
283.4 kb
1,490
106.9 kb
100 bp - 1 kb
26,504
10.8 Mb
10,002
4.2 Mb
1 kb - 10 kb
7,436
14.0 Mb
5,517
14.9 Mb
10 kb - 100 kb
43
595.4 kb
384
6.5 Mb