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Trypanosoma brucei vs Pythium aphanidermatum LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. 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 bruceiPythium aphanidermatum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,064 alignment blocks

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

Uncovered: 24,705,812 out of 25,789,186
Covered: 1,083,374 out of 25,789,186

Uncovered: 12,118,229 out of 13,171,744
Matches: 616,807 out of 13,171,744
Mismatches: 395,941 out of 13,171,744
Insertions: 40,767 out of 13,171,744
Identity over aligned base-pairs: 58.5%

Pythium aphanidermatum

Uncovered: 34,677,509 out of 35,876,849
Covered: 1,199,340 out of 35,876,849

Uncovered: 16,937,107 out of 18,015,574
Matches: 628,945 out of 18,015,574
Mismatches: 400,977 out of 18,015,574
Insertions: 48,545 out of 18,015,574
Identity over aligned base-pairs: 58.3%

Block size distribution

Size range All 3,064 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2
4.0 bp
10 bp - 100 bp
329
23.8 kb
132
9.7 kb
100 bp - 1 kb
2,367
942.2 kb
1,365
650.4 kb
1 kb - 10 kb
366
565.5 kb
472
825.0 kb
10 kb - 100 kb
4
46.4 kb