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Hyaloperonospora arabidopsidis vs Paramecium tetraurelia LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Hyaloperonospora arabidopsidis 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

ParameterHyaloperonospora arabidopsidisParamecium tetraurelia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,411 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Hyaloperonospora arabidopsidis

Uncovered: 78,177,038 out of 78,897,814
Covered: 720,776 out of 78,897,814

Uncovered: 12,540,481 out of 13,171,834
Matches: 364,727 out of 13,171,834
Mismatches: 246,623 out of 13,171,834
Insertions: 20,003 out of 13,171,834
Identity over aligned base-pairs: 57.8%

Paramecium tetraurelia

Uncovered: 70,407,223 out of 72,094,543
Covered: 1,687,320 out of 72,094,543

Uncovered: 52,445,388 out of 54,044,574
Matches: 927,799 out of 54,044,574
Mismatches: 629,864 out of 54,044,574
Insertions: 41,523 out of 54,044,574
Identity over aligned base-pairs: 58.0%

Block size distribution

Size range All 4,411 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7
38.0 bp
10 bp - 100 bp
555
40.9 kb
227
17.6 kb
100 bp - 1 kb
3,469
1.3 Mb
2,192
1.0 Mb
1 kb - 10 kb
380
539.3 kb
591
872.5 kb