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Phaeodactylum tricornutum vs Pythium arrhenomanes LastZ results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) and Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) 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 tricornutumPythium arrhenomanes
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,295 alignment blocks

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

Uncovered: 25,718,743 out of 27,568,093
Covered: 1,849,350 out of 27,568,093

Uncovered: 16,080,842 out of 17,873,974
Matches: 1,067,766 out of 17,873,974
Mismatches: 647,603 out of 17,873,974
Insertions: 77,763 out of 17,873,974
Identity over aligned base-pairs: 59.5%

Pythium arrhenomanes

Uncovered: 42,723,252 out of 44,672,625
Covered: 1,949,373 out of 44,672,625

Uncovered: 16,668,735 out of 18,367,184
Matches: 1,027,923 out of 18,367,184
Mismatches: 607,772 out of 18,367,184
Insertions: 62,754 out of 18,367,184
Identity over aligned base-pairs: 60.5%

Block size distribution

Size range All 5,295 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
13
69.0 bp
10 bp - 100 bp
643
46.1 kb
151
11.2 kb
100 bp - 1 kb
4,131
1.6 Mb
2,133
1.0 Mb
1 kb - 10 kb
508
747.4 kb
816
1.3 Mb
10 kb - 100 kb
1
10.6 kb