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Entamoeba histolytica vs Phytophthora lateralis LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Entamoeba histolytica 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

ParameterEntamoeba histolyticaPhytophthora lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 906 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Entamoeba histolytica

Uncovered: 20,521,692 out of 20,835,395
Covered: 313,703 out of 20,835,395

Uncovered: 9,942,030 out of 10,244,611
Matches: 172,244 out of 10,244,611
Mismatches: 124,813 out of 10,244,611
Insertions: 5,524 out of 10,244,611
Identity over aligned base-pairs: 56.9%

Phytophthora lateralis

Uncovered: 43,721,959 out of 43,981,379
Covered: 259,420 out of 43,981,379

Uncovered: 14,026,543 out of 14,242,768
Matches: 120,698 out of 14,242,768
Mismatches: 89,680 out of 14,242,768
Insertions: 5,847 out of 14,242,768
Identity over aligned base-pairs: 55.8%

Block size distribution

Size range All 906 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1
7.0 bp
10 bp - 100 bp
57
4.1 kb
25
2.0 kb
100 bp - 1 kb
776
288.9 kb
444
188.5 kb
1 kb - 10 kb
72
97.8 kb
133
200.2 kb