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Paramecium tetraurelia vs Pythium iwayamai LastZ results

Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,252 alignment blocks

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

Uncovered: 70,573,186 out of 72,094,543
Covered: 1,521,357 out of 72,094,543

Uncovered: 52,595,187 out of 54,044,574
Matches: 820,523 out of 54,044,574
Mismatches: 598,492 out of 54,044,574
Insertions: 30,372 out of 54,044,574
Identity over aligned base-pairs: 56.6%

Pythium iwayamai

Uncovered: 42,514,915 out of 43,199,174
Covered: 684,259 out of 43,199,174

Uncovered: 18,961,747 out of 19,552,457
Matches: 331,700 out of 19,552,457
Mismatches: 242,316 out of 19,552,457
Insertions: 16,694 out of 19,552,457
Identity over aligned base-pairs: 56.2%

Block size distribution

Size range All 4,252 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
10
49.0 bp
10 bp - 100 bp
543
40.0 kb
214
17.0 kb
100 bp - 1 kb
3,430
1.2 Mb
1,918
851.4 kb
1 kb - 10 kb
269
420.9 kb
417
795.1 kb
10 kb - 100 kb
4
46.5 kb