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Phaeodactylum tricornutum vs Phytophthora lateralis LastZ results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) 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 tricornutumPhytophthora lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,625 alignment blocks

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

Uncovered: 25,995,288 out of 27,568,093
Covered: 1,572,805 out of 27,568,093

Uncovered: 16,349,243 out of 17,873,974
Matches: 909,782 out of 17,873,974
Mismatches: 546,426 out of 17,873,974
Insertions: 68,523 out of 17,873,974
Identity over aligned base-pairs: 59.7%

Phytophthora lateralis

Uncovered: 42,297,702 out of 43,981,379
Covered: 1,683,677 out of 43,981,379

Uncovered: 12,762,763 out of 14,242,768
Matches: 887,394 out of 14,242,768
Mismatches: 537,090 out of 14,242,768
Insertions: 55,521 out of 14,242,768
Identity over aligned base-pairs: 60.0%

Block size distribution

Size range All 4,625 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
6
36.0 bp
10 bp - 100 bp
587
40.2 kb
163
11.5 kb
100 bp - 1 kb
3,574
1.4 Mb
1,769
848.3 kb
1 kb - 10 kb
458
662.8 kb
729
1.2 Mb