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Phytophthora infestans vs Paramecium tetraurelia LastZ results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phytophthora infestans 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 infestansParamecium tetraurelia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,558 alignment blocks

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

Uncovered: 227,115,907 out of 228,543,505
Covered: 1,427,598 out of 228,543,505

Uncovered: 21,359,386 out of 22,421,425
Matches: 605,060 out of 22,421,425
Mismatches: 421,196 out of 22,421,425
Insertions: 35,783 out of 22,421,425
Identity over aligned base-pairs: 57.0%

Paramecium tetraurelia

Uncovered: 69,656,637 out of 72,094,543
Covered: 2,437,906 out of 72,094,543

Uncovered: 51,746,099 out of 54,044,574
Matches: 1,277,375 out of 54,044,574
Mismatches: 959,434 out of 54,044,574
Insertions: 61,666 out of 54,044,574
Identity over aligned base-pairs: 55.6%

Block size distribution

Size range All 8,558 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
52
115.0 bp
10 bp - 100 bp
2,372
191.1 kb
1,859
153.5 kb
100 bp - 1 kb
5,508
1.9 Mb
3,584
1.4 Mb
1 kb - 10 kb
621
952.0 kb
793
1.4 Mb
10 kb - 100 kb
5
85.7 kb
10
159.4 kb