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Paramecium tetraurelia vs Emiliania huxleyi LastZ results

Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) and Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. 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 tetraureliaEmiliania huxleyi
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,179 alignment blocks

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

Uncovered: 71,400,733 out of 72,094,543
Covered: 693,810 out of 72,094,543

Uncovered: 53,382,396 out of 54,044,574
Matches: 380,170 out of 54,044,574
Mismatches: 271,584 out of 54,044,574
Insertions: 10,424 out of 54,044,574
Identity over aligned base-pairs: 57.4%

Emiliania huxleyi

Uncovered: 167,235,856 out of 167,675,649
Covered: 439,793 out of 167,675,649

Uncovered: 39,341,882 out of 39,740,234
Matches: 235,075 out of 39,740,234
Mismatches: 157,807 out of 39,740,234
Insertions: 5,470 out of 39,740,234
Identity over aligned base-pairs: 59.0%

Block size distribution

Size range All 3,179 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
10
61.0 bp
10 bp - 100 bp
513
37.9 kb
175
14.0 kb
100 bp - 1 kb
2,551
764.6 kb
1,364
507.4 kb
1 kb - 10 kb
105
133.5 kb
248
414.6 kb