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Paramecium tetraurelia vs Phytophthora kernoviae LastZ results

Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) and Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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 kernoviae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 6,255 alignment blocks

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

Uncovered: 69,640,862 out of 72,094,543
Covered: 2,453,681 out of 72,094,543

Uncovered: 51,703,118 out of 54,044,574
Matches: 1,350,349 out of 54,044,574
Mismatches: 922,486 out of 54,044,574
Insertions: 68,621 out of 54,044,574
Identity over aligned base-pairs: 57.7%

Phytophthora kernoviae

Uncovered: 42,069,192 out of 43,208,681
Covered: 1,139,489 out of 43,208,681

Uncovered: 10,583,517 out of 11,344,308
Matches: 432,526 out of 11,344,308
Mismatches: 304,474 out of 11,344,308
Insertions: 23,791 out of 11,344,308
Identity over aligned base-pairs: 56.9%

Block size distribution

Size range All 6,255 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
13
49.0 bp
10 bp - 100 bp
688
49.2 kb
243
18.9 kb
100 bp - 1 kb
4,947
1.9 Mb
2,857
1.3 Mb
1 kb - 10 kb
607
915.4 kb
819
1.5 Mb
10 kb - 100 kb
5
60.9 kb