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Hyaloperonospora arabidopsidis vs Phaeodactylum tricornutum LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Hyaloperonospora arabidopsidis 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

ParameterHyaloperonospora arabidopsidisPhaeodactylum tricornutum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,118 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Hyaloperonospora arabidopsidis

Uncovered: 77,050,065 out of 78,897,814
Covered: 1,847,749 out of 78,897,814

Uncovered: 11,580,690 out of 13,171,834
Matches: 964,366 out of 13,171,834
Mismatches: 572,852 out of 13,171,834
Insertions: 53,926 out of 13,171,834
Identity over aligned base-pairs: 60.6%

Phaeodactylum tricornutum

Uncovered: 25,823,828 out of 27,568,093
Covered: 1,744,265 out of 27,568,093

Uncovered: 16,200,940 out of 17,873,974
Matches: 1,001,195 out of 17,873,974
Mismatches: 602,744 out of 17,873,974
Insertions: 69,095 out of 17,873,974
Identity over aligned base-pairs: 59.8%

Block size distribution

Size range All 5,118 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5
40.0 bp
10 bp - 100 bp
747
54.3 kb
242
18.9 kb
100 bp - 1 kb
3,872
1.4 Mb
1,893
891.0 kb
1 kb - 10 kb
494
726.1 kb
807
1.3 Mb