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Trypanosoma brucei vs Phytophthora lateralis LastZ results

Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) 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 lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 2,526 alignment blocks

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

Uncovered: 24,896,355 out of 25,789,186
Covered: 892,831 out of 25,789,186

Uncovered: 12,305,507 out of 13,171,744
Matches: 509,733 out of 13,171,744
Mismatches: 322,635 out of 13,171,744
Insertions: 33,869 out of 13,171,744
Identity over aligned base-pairs: 58.8%

Phytophthora lateralis

Uncovered: 43,041,604 out of 43,981,379
Covered: 939,775 out of 43,981,379

Uncovered: 13,427,333 out of 14,242,768
Matches: 474,263 out of 14,242,768
Mismatches: 304,043 out of 14,242,768
Insertions: 37,129 out of 14,242,768
Identity over aligned base-pairs: 58.2%

Block size distribution

Size range All 2,526 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4
25.0 bp
10 bp - 100 bp
293
20.8 kb
117
8.7 kb
100 bp - 1 kb
1,944
768.3 kb
1,159
539.6 kb
1 kb - 10 kb
285
434.8 kb
354
629.0 kb
10 kb - 100 kb
4
46.7 kb