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Pythium ultimum vs Trypanosoma brucei LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Pythium ultimum 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

ParameterPythium ultimumTrypanosoma brucei
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,447 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium ultimum

Uncovered: 43,619,115 out of 44,913,582
Covered: 1,294,467 out of 44,913,582

Uncovered: 18,731,676 out of 19,826,256
Matches: 638,214 out of 19,826,256
Mismatches: 409,587 out of 19,826,256
Insertions: 46,779 out of 19,826,256
Identity over aligned base-pairs: 58.3%

Trypanosoma brucei

Uncovered: 24,669,228 out of 25,789,186
Covered: 1,119,958 out of 25,789,186

Uncovered: 12,113,579 out of 13,171,744
Matches: 606,479 out of 13,171,744
Mismatches: 411,801 out of 13,171,744
Insertions: 39,885 out of 13,171,744
Identity over aligned base-pairs: 57.3%

Block size distribution

Size range All 3,447 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7
49.0 bp
10 bp - 100 bp
507
38.5 kb
245
19.8 kb
100 bp - 1 kb
2,574
985.0 kb
1,509
688.4 kb
1 kb - 10 kb
355
561.0 kb
462
830.5 kb
10 kb - 100 kb
4
96.9 kb
7
142.9 kb