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Albugo laibachii vs Phaeodactylum tricornutum LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Albugo laibachii 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

ParameterAlbugo laibachiiPhaeodactylum tricornutum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,673 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Albugo laibachii

Uncovered: 31,057,503 out of 32,766,811
Covered: 1,709,308 out of 32,766,811

Uncovered: 14,347,097 out of 15,902,867
Matches: 937,521 out of 15,902,867
Mismatches: 563,577 out of 15,902,867
Insertions: 54,672 out of 15,902,867
Identity over aligned base-pairs: 60.3%

Phaeodactylum tricornutum

Uncovered: 26,025,482 out of 27,568,093
Covered: 1,542,611 out of 27,568,093

Uncovered: 16,402,223 out of 17,873,974
Matches: 884,645 out of 17,873,974
Mismatches: 528,866 out of 17,873,974
Insertions: 58,240 out of 17,873,974
Identity over aligned base-pairs: 60.1%

Block size distribution

Size range All 4,673 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
8
48.0 bp
10 bp - 100 bp
676
47.8 kb
172
13.0 kb
100 bp - 1 kb
3,549
1.3 Mb
1,670
800.3 kb
1 kb - 10 kb
440
662.0 kb
740
1.2 Mb
10 kb - 100 kb
1
10.4 kb