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Magnaporthe oryzae vs Saccharomyces cerevisiae LastZ results

Magnaporthe oryzae (Magnaporthe oryzae 70-15, MG8) and Saccharomyces cerevisiae (Saccharomyces cerevisiae S288c, R64-1-1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Magnaporthe oryzae 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

ParameterMagnaporthe oryzaeSaccharomyces cerevisiae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,407 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Magnaporthe oryzae

Uncovered: 39,378,506 out of 41,027,733
Covered: 1,649,227 out of 41,027,733

Uncovered: 15,144,580 out of 16,744,523
Matches: 943,872 out of 16,744,523
Mismatches: 603,148 out of 16,744,523
Insertions: 52,923 out of 16,744,523
Identity over aligned base-pairs: 59.0%

Saccharomyces cerevisiae

Uncovered: 10,327,946 out of 12,157,105
Covered: 1,829,159 out of 12,157,105

Uncovered: 6,782,545 out of 8,596,583
Matches: 1,084,087 out of 8,596,583
Mismatches: 684,895 out of 8,596,583
Insertions: 45,056 out of 8,596,583
Identity over aligned base-pairs: 59.8%

Block size distribution

Size range All 4,407 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
14
75.0 bp
10 bp - 100 bp
565
40.4 kb
104
8.1 kb
100 bp - 1 kb
3,340
1.3 Mb
1,322
685.8 kb
1 kb - 10 kb
488
742.7 kb
778
1.4 Mb