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Trypanosoma brucei vs Emiliania huxleyi LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) 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 bruceiEmiliania huxleyi
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,219 alignment blocks

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

Uncovered: 25,049,801 out of 25,789,186
Covered: 739,385 out of 25,789,186

Uncovered: 12,500,702 out of 13,171,744
Matches: 398,562 out of 13,171,744
Mismatches: 252,807 out of 13,171,744
Insertions: 19,673 out of 13,171,744
Identity over aligned base-pairs: 59.4%

Emiliania huxleyi

Uncovered: 166,503,468 out of 167,675,649
Covered: 1,172,181 out of 167,675,649

Uncovered: 38,781,251 out of 39,740,234
Matches: 581,281 out of 39,740,234
Mismatches: 343,786 out of 39,740,234
Insertions: 33,916 out of 39,740,234
Identity over aligned base-pairs: 60.6%

Block size distribution

Size range All 5,219 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
16
89.0 bp
10 bp - 100 bp
1,049
73.4 kb
297
22.7 kb
100 bp - 1 kb
4,026
1.2 Mb
1,998
805.4 kb
1 kb - 10 kb
128
179.0 kb
327
615.1 kb
10 kb - 100 kb
4
40.9 kb