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Magnaporthe oryzae vs Schizosaccharomyces pombe LastZ results

Magnaporthe oryzae (Magnaporthe oryzae 70-15, MG8) and Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) 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 oryzaeSchizosaccharomyces pombe
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,551 alignment blocks

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

Uncovered: 39,188,852 out of 41,027,733
Covered: 1,838,881 out of 41,027,733

Uncovered: 14,964,263 out of 16,744,523
Matches: 1,047,660 out of 16,744,523
Mismatches: 670,492 out of 16,744,523
Insertions: 62,108 out of 16,744,523
Identity over aligned base-pairs: 58.8%

Schizosaccharomyces pombe

Uncovered: 10,758,058 out of 12,631,379
Covered: 1,873,321 out of 12,631,379

Uncovered: 5,333,676 out of 7,176,702
Matches: 1,107,820 out of 7,176,702
Mismatches: 699,888 out of 7,176,702
Insertions: 35,318 out of 7,176,702
Identity over aligned base-pairs: 60.1%

Block size distribution

Size range All 4,551 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
10
49.0 bp
10 bp - 100 bp
577
40.7 kb
51
3.9 kb
100 bp - 1 kb
3,484
1.3 Mb
1,316
713.1 kb
1 kb - 10 kb
480
760.1 kb
787
1.4 Mb