In this section

Trypanosoma brucei vs Phytophthora parasitica LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_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 bruceiPhytophthora parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,107 alignment blocks

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

Uncovered: 24,730,131 out of 25,789,186
Covered: 1,059,055 out of 25,789,186

Uncovered: 12,126,944 out of 13,171,744
Matches: 616,640 out of 13,171,744
Mismatches: 387,757 out of 13,171,744
Insertions: 40,403 out of 13,171,744
Identity over aligned base-pairs: 59.0%

Phytophthora parasitica

Uncovered: 53,996,163 out of 55,229,644
Covered: 1,233,481 out of 55,229,644

Uncovered: 26,399,262 out of 27,601,672
Matches: 700,839 out of 27,601,672
Mismatches: 447,740 out of 27,601,672
Insertions: 53,831 out of 27,601,672
Identity over aligned base-pairs: 58.3%

Block size distribution

Size range All 3,107 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7
35.0 bp
10 bp - 100 bp
303
21.5 kb
115
8.2 kb
100 bp - 1 kb
2,419
965.5 kb
1,433
675.2 kb
1 kb - 10 kb
378
584.3 kb
485
841.3 kb
10 kb - 100 kb
4
46.6 kb