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Paramecium tetraurelia vs Phytophthora lateralis LastZ results

Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) 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 tetraureliaPhytophthora lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,632 alignment blocks

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

Uncovered: 70,328,277 out of 72,094,543
Covered: 1,766,266 out of 72,094,543

Uncovered: 52,359,779 out of 54,044,574
Matches: 960,628 out of 54,044,574
Mismatches: 681,141 out of 54,044,574
Insertions: 43,026 out of 54,044,574
Identity over aligned base-pairs: 57.0%

Phytophthora lateralis

Uncovered: 43,226,736 out of 43,981,379
Covered: 754,643 out of 43,981,379

Uncovered: 13,614,701 out of 14,242,768
Matches: 353,091 out of 14,242,768
Mismatches: 254,918 out of 14,242,768
Insertions: 20,058 out of 14,242,768
Identity over aligned base-pairs: 56.2%

Block size distribution

Size range All 4,632 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15
63.0 bp
10 bp - 100 bp
515
37.4 kb
213
16.5 kb
100 bp - 1 kb
3,732
1.4 Mb
2,118
967.2 kb
1 kb - 10 kb
370
569.3 kb
525
974.1 kb
10 kb - 100 kb
5
55.8 kb