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Phytophthora ramorum vs Trypanosoma brucei LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phytophthora ramorum 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

ParameterPhytophthora ramorumTrypanosoma brucei
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,220 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora ramorum

Uncovered: 65,307,468 out of 66,652,401
Covered: 1,344,933 out of 66,652,401

Uncovered: 21,152,632 out of 22,377,278
Matches: 715,825 out of 22,377,278
Mismatches: 454,287 out of 22,377,278
Insertions: 54,534 out of 22,377,278
Identity over aligned base-pairs: 58.5%

Trypanosoma brucei

Uncovered: 24,681,507 out of 25,789,186
Covered: 1,107,679 out of 25,789,186

Uncovered: 12,115,047 out of 13,171,744
Matches: 605,671 out of 13,171,744
Mismatches: 411,639 out of 13,171,744
Insertions: 39,387 out of 13,171,744
Identity over aligned base-pairs: 57.3%

Block size distribution

Size range All 3,220 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2
5.0 bp
10 bp - 100 bp
419
30.1 kb
186
13.7 kb
100 bp - 1 kb
2,372
967.2 kb
1,447
690.4 kb
1 kb - 10 kb
427
703.0 kb
511
927.0 kb
10 kb - 100 kb
6
69.2 kb