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Albugo laibachii vs Entamoeba histolytica LastZ results

Albugo laibachii (Albugo laibachii, ENA1) and Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Albugo laibachii 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

ParameterAlbugo laibachiiEntamoeba histolytica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,213 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Albugo laibachii

Uncovered: 32,083,687 out of 32,766,811
Covered: 683,124 out of 32,766,811

Uncovered: 15,269,835 out of 15,902,867
Matches: 368,885 out of 15,902,867
Mismatches: 234,311 out of 15,902,867
Insertions: 29,836 out of 15,902,867
Identity over aligned base-pairs: 58.3%

Entamoeba histolytica

Uncovered: 20,080,415 out of 20,835,395
Covered: 754,980 out of 20,835,395

Uncovered: 9,526,035 out of 10,244,611
Matches: 431,420 out of 10,244,611
Mismatches: 268,128 out of 10,244,611
Insertions: 19,028 out of 10,244,611
Identity over aligned base-pairs: 60.0%

Block size distribution

Size range All 2,213 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4
13.0 bp
10 bp - 100 bp
225
16.2 kb
73
5.7 kb
100 bp - 1 kb
1,745
672.0 kb
1,071
483.0 kb
1 kb - 10 kb
239
350.7 kb
347
550.2 kb