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Phytophthora ramorum vs Paramecium tetraurelia LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) 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 ramorumParamecium tetraurelia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,524 alignment blocks

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

Uncovered: 65,607,367 out of 66,652,401
Covered: 1,045,034 out of 66,652,401

Uncovered: 21,432,631 out of 22,377,278
Matches: 532,149 out of 22,377,278
Mismatches: 383,341 out of 22,377,278
Insertions: 29,157 out of 22,377,278
Identity over aligned base-pairs: 56.3%

Paramecium tetraurelia

Uncovered: 69,971,940 out of 72,094,543
Covered: 2,122,603 out of 72,094,543

Uncovered: 52,032,416 out of 54,044,574
Matches: 1,125,368 out of 54,044,574
Mismatches: 836,893 out of 54,044,574
Insertions: 49,897 out of 54,044,574
Identity over aligned base-pairs: 55.9%

Block size distribution

Size range All 5,524 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
14
49.0 bp
10 bp - 100 bp
651
46.9 kb
282
21.8 kb
100 bp - 1 kb
4,326
1.6 Mb
2,447
1.1 Mb
1 kb - 10 kb
533
838.4 kb
702
1.3 Mb
10 kb - 100 kb
6
66.8 kb