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Paramecium tetraurelia vs Phytophthora parasitica LastZ results

Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Paramecium tetraurelia 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

ParameterParamecium tetraureliaPhytophthora parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 6,109 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Paramecium tetraurelia

Uncovered: 69,684,645 out of 72,094,543
Covered: 2,409,898 out of 72,094,543

Uncovered: 51,744,416 out of 54,044,574
Matches: 1,327,943 out of 54,044,574
Mismatches: 907,857 out of 54,044,574
Insertions: 64,358 out of 54,044,574
Identity over aligned base-pairs: 57.7%

Phytophthora parasitica

Uncovered: 54,101,700 out of 55,229,644
Covered: 1,127,944 out of 55,229,644

Uncovered: 26,508,399 out of 27,601,672
Matches: 620,096 out of 27,601,672
Mismatches: 434,113 out of 27,601,672
Insertions: 39,064 out of 27,601,672
Identity over aligned base-pairs: 56.7%

Block size distribution

Size range All 6,109 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
11
39.0 bp
10 bp - 100 bp
657
47.9 kb
229
17.5 kb
100 bp - 1 kb
4,849
1.9 Mb
2,844
1.3 Mb
1 kb - 10 kb
592
912.6 kb
789
1.4 Mb
10 kb - 100 kb
5
59.5 kb