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Trypanosoma brucei vs Pythium vexans LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Pythium vexans (Pythium vexans DAOM BR484, pve_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 vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,030 alignment blocks

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

Uncovered: 24,756,587 out of 25,789,186
Covered: 1,032,599 out of 25,789,186

Uncovered: 12,148,010 out of 13,171,744
Matches: 604,066 out of 13,171,744
Mismatches: 380,143 out of 13,171,744
Insertions: 39,525 out of 13,171,744
Identity over aligned base-pairs: 59.0%

Pythium vexans

Uncovered: 32,671,433 out of 33,844,883
Covered: 1,173,450 out of 33,844,883

Uncovered: 17,547,352 out of 18,608,353
Matches: 618,238 out of 18,608,353
Mismatches: 394,153 out of 18,608,353
Insertions: 48,610 out of 18,608,353
Identity over aligned base-pairs: 58.3%

Block size distribution

Size range All 3,030 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9
58.0 bp
10 bp - 100 bp
341
24.5 kb
102
7.3 kb
100 bp - 1 kb
2,324
895.6 kb
1,354
632.0 kb
1 kb - 10 kb
356
568.4 kb
441
803.3 kb
10 kb - 100 kb
4
45.9 kb