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Phytophthora ramorum vs Phaeodactylum tricornutum LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phytophthora ramorum 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

ParameterPhytophthora ramorumPhaeodactylum tricornutum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 6,124 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora ramorum

Uncovered: 64,195,161 out of 66,652,401
Covered: 2,457,240 out of 66,652,401

Uncovered: 20,155,927 out of 22,377,278
Matches: 1,341,179 out of 22,377,278
Mismatches: 802,527 out of 22,377,278
Insertions: 77,645 out of 22,377,278
Identity over aligned base-pairs: 60.4%

Phaeodactylum tricornutum

Uncovered: 25,543,601 out of 27,568,093
Covered: 2,024,492 out of 27,568,093

Uncovered: 15,946,048 out of 17,873,974
Matches: 1,111,460 out of 17,873,974
Mismatches: 733,046 out of 17,873,974
Insertions: 83,420 out of 17,873,974
Identity over aligned base-pairs: 57.7%

Block size distribution

Size range All 6,124 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9
38.0 bp
10 bp - 100 bp
763
53.9 kb
217
16.0 kb
100 bp - 1 kb
4,683
1.8 Mb
2,265
1.1 Mb
1 kb - 10 kb
666
1.0 Mb
1,045
1.8 Mb
10 kb - 100 kb
3
53.3 kb
4
69.9 kb