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Phaeodactylum tricornutum vs Phytophthora infestans LastZ results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) and Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) 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 infestans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 9,591 alignment blocks

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

Uncovered: 25,508,792 out of 27,568,093
Covered: 2,059,301 out of 27,568,093

Uncovered: 15,949,266 out of 17,873,974
Matches: 1,098,695 out of 17,873,974
Mismatches: 744,314 out of 17,873,974
Insertions: 81,699 out of 17,873,974
Identity over aligned base-pairs: 57.1%

Phytophthora infestans

Uncovered: 225,427,464 out of 228,543,505
Covered: 3,116,041 out of 228,543,505

Uncovered: 20,257,506 out of 22,421,425
Matches: 1,305,006 out of 22,421,425
Mismatches: 782,526 out of 22,421,425
Insertions: 76,387 out of 22,421,425
Identity over aligned base-pairs: 60.3%

Block size distribution

Size range All 9,591 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
21
129.0 bp
10 bp - 100 bp
3,077
228.3 kb
2,323
180.6 kb
100 bp - 1 kb
5,730
2.0 Mb
3,157
1.3 Mb
1 kb - 10 kb
757
1.2 Mb
1,103
2.0 Mb
10 kb - 100 kb
6
126.6 kb
8
161.2 kb