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Trypanosoma brucei vs Pythium arrhenomanes LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_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 arrhenomanes
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,815 alignment blocks

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

Uncovered: 24,781,364 out of 25,789,186
Covered: 1,007,822 out of 25,789,186

Uncovered: 12,177,088 out of 13,171,744
Matches: 580,131 out of 13,171,744
Mismatches: 377,063 out of 13,171,744
Insertions: 37,462 out of 13,171,744
Identity over aligned base-pairs: 58.3%

Pythium arrhenomanes

Uncovered: 43,557,032 out of 44,672,625
Covered: 1,115,593 out of 44,672,625

Uncovered: 17,392,792 out of 18,367,184
Matches: 567,776 out of 18,367,184
Mismatches: 362,620 out of 18,367,184
Insertions: 43,996 out of 18,367,184
Identity over aligned base-pairs: 58.3%

Block size distribution

Size range All 2,815 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4
22.0 bp
10 bp - 100 bp
292
21.8 kb
102
7.9 kb
100 bp - 1 kb
2,178
868.8 kb
1,359
646.9 kb
1 kb - 10 kb
341
526.8 kb
406
738.9 kb
10 kb - 100 kb
2
23.9 kb