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Fusarium verticillioides vs Schizosaccharomyces pombe LastZ results

Fusarium verticillioides (Fusarium verticillioides 7600, ASM14955v1) and Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Fusarium verticillioides 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 verticillioidesSchizosaccharomyces pombe
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,226 alignment blocks

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

Uncovered: 39,471,251 out of 41,885,085
Covered: 2,413,834 out of 41,885,085

Uncovered: 15,658,320 out of 17,841,847
Matches: 1,290,704 out of 17,841,847
Mismatches: 807,243 out of 17,841,847
Insertions: 85,580 out of 17,841,847
Identity over aligned base-pairs: 59.1%

Schizosaccharomyces pombe

Uncovered: 10,451,705 out of 12,631,379
Covered: 2,179,674 out of 12,631,379

Uncovered: 5,061,242 out of 7,176,702
Matches: 1,279,256 out of 7,176,702
Mismatches: 788,828 out of 7,176,702
Insertions: 47,376 out of 7,176,702
Identity over aligned base-pairs: 60.5%

Block size distribution

Size range All 5,226 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
6
39.0 bp
10 bp - 100 bp
675
48.3 kb
138
10.6 kb
100 bp - 1 kb
3,790
1.5 Mb
1,533
834.2 kb
1 kb - 10 kb
755
1.2 Mb
1,071
1.9 Mb
10 kb - 100 kb
3
34.8 kb