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Fusarium solani vs Schizosaccharomyces pombe LastZ results

Fusarium solani (Fusarium solani mpVI 77-13-4, v2.0) and Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Fusarium solani 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

ParameterFusarium solaniSchizosaccharomyces pombe
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,322 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Fusarium solani

Uncovered: 48,864,954 out of 51,291,997
Covered: 2,427,043 out of 51,291,997

Uncovered: 20,345,783 out of 22,633,081
Matches: 1,341,329 out of 22,633,081
Mismatches: 859,734 out of 22,633,081
Insertions: 86,235 out of 22,633,081
Identity over aligned base-pairs: 58.6%

Schizosaccharomyces pombe

Uncovered: 10,581,333 out of 12,631,379
Covered: 2,050,046 out of 12,631,379

Uncovered: 5,163,869 out of 7,176,702
Matches: 1,209,142 out of 7,176,702
Mismatches: 760,773 out of 7,176,702
Insertions: 42,918 out of 7,176,702
Identity over aligned base-pairs: 60.1%

Block size distribution

Size range All 5,322 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7
50.0 bp
10 bp - 100 bp
630
44.0 kb
113
8.5 kb
100 bp - 1 kb
3,962
1.6 Mb
1,563
843.2 kb
1 kb - 10 kb
723
1.1 Mb
1,098
1.9 Mb