In this section

Pythium ultimum vs Pythium arrhenomanes LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) 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 ultimumPythium arrhenomanes
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 39,731 alignment blocks

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

Uncovered: 23,725,439 out of 44,913,582
Covered: 21,188,143 out of 44,913,582

Uncovered: 4,045,240 out of 19,826,256
Matches: 10,228,071 out of 19,826,256
Mismatches: 4,928,383 out of 19,826,256
Insertions: 624,562 out of 19,826,256
Identity over aligned base-pairs: 64.8%

Pythium arrhenomanes

Uncovered: 24,996,505 out of 44,672,625
Covered: 19,676,120 out of 44,672,625

Uncovered: 4,001,958 out of 18,367,184
Matches: 9,478,145 out of 18,367,184
Mismatches: 4,355,763 out of 18,367,184
Insertions: 531,318 out of 18,367,184
Identity over aligned base-pairs: 66.0%

Block size distribution

Size range All 39,731 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
165
862.0 bp
10 bp - 100 bp
4,581
305.2 kb
1,371
96.2 kb
100 bp - 1 kb
27,466
11.4 Mb
9,242
4.1 Mb
1 kb - 10 kb
7,498
13.2 Mb
6,205
16.5 Mb
10 kb - 100 kb
21
272.5 kb
291
4.4 Mb