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Trypanosoma brucei vs Phytophthora infestans LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) 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 infestans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 6,460 alignment blocks

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

Uncovered: 24,667,760 out of 25,789,186
Covered: 1,121,426 out of 25,789,186

Uncovered: 12,120,304 out of 13,171,744
Matches: 607,648 out of 13,171,744
Mismatches: 404,815 out of 13,171,744
Insertions: 38,977 out of 13,171,744
Identity over aligned base-pairs: 57.8%

Phytophthora infestans

Uncovered: 226,920,608 out of 228,543,505
Covered: 1,622,897 out of 228,543,505

Uncovered: 21,212,090 out of 22,421,425
Matches: 706,266 out of 22,421,425
Mismatches: 450,212 out of 22,421,425
Insertions: 52,857 out of 22,421,425
Identity over aligned base-pairs: 58.4%

Block size distribution

Size range All 6,460 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7
53.0 bp
10 bp - 100 bp
3,250
256.3 kb
2,933
234.5 kb
100 bp - 1 kb
2,796
1.0 Mb
1,895
756.8 kb
1 kb - 10 kb
402
636.6 kb
501
878.6 kb
10 kb - 100 kb
5
74.2 kb
8
132.0 kb