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Paramecium tetraurelia vs Pythium arrhenomanes LastZ results

Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) and Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_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 arrhenomanes
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,279 alignment blocks

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

Uncovered: 70,474,114 out of 72,094,543
Covered: 1,620,429 out of 72,094,543

Uncovered: 52,491,960 out of 54,044,574
Matches: 879,242 out of 54,044,574
Mismatches: 639,066 out of 54,044,574
Insertions: 34,306 out of 54,044,574
Identity over aligned base-pairs: 56.6%

Pythium arrhenomanes

Uncovered: 43,934,090 out of 44,672,625
Covered: 738,535 out of 44,672,625

Uncovered: 17,727,052 out of 18,367,184
Matches: 359,884 out of 18,367,184
Mismatches: 261,476 out of 18,367,184
Insertions: 18,772 out of 18,367,184
Identity over aligned base-pairs: 56.2%

Block size distribution

Size range All 4,279 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9
46.0 bp
10 bp - 100 bp
487
35.2 kb
163
12.7 kb
100 bp - 1 kb
3,413
1.3 Mb
2,000
881.3 kb
1 kb - 10 kb
370
528.1 kb
497
918.8 kb
10 kb - 100 kb
2
22.8 kb