In this section

Trypanosoma brucei vs Entamoeba histolytica LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Entamoeba histolytica (Entamoeba histolytica, JCVI-ESG2-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Trypanosoma brucei 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

ParameterTrypanosoma bruceiEntamoeba histolytica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,381 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Trypanosoma brucei

Uncovered: 25,368,521 out of 25,789,186
Covered: 420,665 out of 25,789,186

Uncovered: 12,799,788 out of 13,171,744
Matches: 213,846 out of 13,171,744
Mismatches: 146,451 out of 13,171,744
Insertions: 11,659 out of 13,171,744
Identity over aligned base-pairs: 57.5%

Entamoeba histolytica

Uncovered: 20,338,371 out of 20,835,395
Covered: 497,024 out of 20,835,395

Uncovered: 9,773,468 out of 10,244,611
Matches: 274,324 out of 10,244,611
Mismatches: 185,556 out of 10,244,611
Insertions: 11,263 out of 10,244,611
Identity over aligned base-pairs: 58.2%

Block size distribution

Size range All 1,381 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
98
7.5 kb
47
3.9 kb
100 bp - 1 kb
1,156
471.7 kb
686
323.1 kb
1 kb - 10 kb
126
176.6 kb
225
328.8 kb