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Hyaloperonospora arabidopsidis vs Entamoeba histolytica LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Hyaloperonospora arabidopsidis 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

ParameterHyaloperonospora arabidopsidisEntamoeba histolytica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,444 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Hyaloperonospora arabidopsidis

Uncovered: 78,481,990 out of 78,897,814
Covered: 415,824 out of 78,897,814

Uncovered: 12,801,661 out of 13,171,834
Matches: 210,546 out of 13,171,834
Mismatches: 147,933 out of 13,171,834
Insertions: 11,694 out of 13,171,834
Identity over aligned base-pairs: 56.9%

Entamoeba histolytica

Uncovered: 20,355,823 out of 20,835,395
Covered: 479,572 out of 20,835,395

Uncovered: 9,781,703 out of 10,244,611
Matches: 269,084 out of 10,244,611
Mismatches: 185,898 out of 10,244,611
Insertions: 7,926 out of 10,244,611
Identity over aligned base-pairs: 58.1%

Block size distribution

Size range All 1,444 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3
19.0 bp
10 bp - 100 bp
146
10.6 kb
72
5.3 kb
100 bp - 1 kb
1,186
450.9 kb
690
310.1 kb
1 kb - 10 kb
109
157.8 kb
206
303.8 kb