In this section

Phytophthora ramorum vs Entamoeba histolytica LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phytophthora ramorum 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 ramorumEntamoeba histolytica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,199 alignment blocks

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

Uncovered: 66,283,918 out of 66,652,401
Covered: 368,483 out of 66,652,401

Uncovered: 22,043,388 out of 22,377,278
Matches: 186,621 out of 22,377,278
Mismatches: 138,660 out of 22,377,278
Insertions: 8,609 out of 22,377,278
Identity over aligned base-pairs: 55.9%

Entamoeba histolytica

Uncovered: 20,420,890 out of 20,835,395
Covered: 414,505 out of 20,835,395

Uncovered: 9,855,873 out of 10,244,611
Matches: 212,558 out of 10,244,611
Mismatches: 170,060 out of 10,244,611
Insertions: 6,120 out of 10,244,611
Identity over aligned base-pairs: 54.7%

Block size distribution

Size range All 1,199 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1
2.0 bp
10 bp - 100 bp
89
6.4 kb
40
3.1 kb
100 bp - 1 kb
997
370.3 kb
565
240.5 kb
1 kb - 10 kb
112
171.9 kb
191
305.2 kb