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Phytophthora kernoviae vs Giardia intestinalis - GCA_000002435.2 LastZ results

Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. Phytophthora kernoviae 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

ParameterPhytophthora kernoviaeGiardia intestinalis - GCA_000002435.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,522 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora kernoviae

Uncovered: 42,624,746 out of 43,208,681
Covered: 583,935 out of 43,208,681

Uncovered: 10,928,680 out of 11,344,308
Matches: 245,740 out of 11,344,308
Mismatches: 155,078 out of 11,344,308
Insertions: 14,810 out of 11,344,308
Identity over aligned base-pairs: 59.1%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,681,245 out of 12,078,186
Covered: 396,941 out of 12,078,186

Uncovered: 9,076,684 out of 9,469,365
Matches: 229,308 out of 9,469,365
Mismatches: 144,796 out of 9,469,365
Insertions: 18,577 out of 9,469,365
Identity over aligned base-pairs: 58.4%

Block size distribution

Size range All 1,522 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4
16.0 bp
10 bp - 100 bp
193
13.9 kb
68
5.2 kb
100 bp - 1 kb
1,177
441.3 kb
713
321.1 kb
1 kb - 10 kb
148
219.2 kb
185
348.1 kb