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Paramecium tetraurelia vs Pythium vexans LastZ results

Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) and Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_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 tetraureliaPythium vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,451 alignment blocks

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

Uncovered: 70,466,866 out of 72,094,543
Covered: 1,627,677 out of 72,094,543

Uncovered: 52,488,361 out of 54,044,574
Matches: 882,768 out of 54,044,574
Mismatches: 639,407 out of 54,044,574
Insertions: 34,038 out of 54,044,574
Identity over aligned base-pairs: 56.7%

Pythium vexans

Uncovered: 33,097,403 out of 33,844,883
Covered: 747,480 out of 33,844,883

Uncovered: 17,930,943 out of 18,608,353
Matches: 378,759 out of 18,608,353
Mismatches: 279,520 out of 18,608,353
Insertions: 19,131 out of 18,608,353
Identity over aligned base-pairs: 55.9%

Block size distribution

Size range All 4,451 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
20
67.0 bp
10 bp - 100 bp
524
39.0 kb
156
12.3 kb
100 bp - 1 kb
3,517
1.3 Mb
2,004
878.3 kb
1 kb - 10 kb
390
568.9 kb
494
933.1 kb
10 kb - 100 kb
3
35.6 kb