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Entamoeba histolytica vs Pythium arrhenomanes LastZ results

Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) and Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) 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 histolyticaPythium arrhenomanes
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 876 alignment blocks

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

Uncovered: 20,511,634 out of 20,835,395
Covered: 323,761 out of 20,835,395

Uncovered: 9,932,040 out of 10,244,611
Matches: 173,576 out of 10,244,611
Mismatches: 134,385 out of 10,244,611
Insertions: 4,610 out of 10,244,611
Identity over aligned base-pairs: 55.5%

Pythium arrhenomanes

Uncovered: 44,431,266 out of 44,672,625
Covered: 241,359 out of 44,672,625

Uncovered: 18,153,583 out of 18,367,184
Matches: 118,887 out of 18,367,184
Mismatches: 89,779 out of 18,367,184
Insertions: 4,935 out of 18,367,184
Identity over aligned base-pairs: 55.7%

Block size distribution

Size range All 876 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1
9.0 bp
10 bp - 100 bp
63
4.6 kb
13
992.0 bp
100 bp - 1 kb
739
278.8 kb
468
199.4 kb
1 kb - 10 kb
73
99.1 kb
127
182.0 kb