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Fusarium verticillioides vs Saccharomyces cerevisiae LastZ results

Fusarium verticillioides (Fusarium verticillioides 7600, ASM14955v1) and Saccharomyces cerevisiae (Saccharomyces cerevisiae S288c, R64-1-1) 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 verticillioidesSaccharomyces cerevisiae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,046 alignment blocks

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

Uncovered: 39,716,973 out of 41,885,085
Covered: 2,168,112 out of 41,885,085

Uncovered: 15,876,356 out of 17,841,847
Matches: 1,158,534 out of 17,841,847
Mismatches: 733,680 out of 17,841,847
Insertions: 73,277 out of 17,841,847
Identity over aligned base-pairs: 58.9%

Saccharomyces cerevisiae

Uncovered: 10,047,834 out of 12,157,105
Covered: 2,109,271 out of 12,157,105

Uncovered: 6,525,935 out of 8,596,583
Matches: 1,238,769 out of 8,596,583
Mismatches: 772,157 out of 8,596,583
Insertions: 59,722 out of 8,596,583
Identity over aligned base-pairs: 59.8%

Block size distribution

Size range All 5,046 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
12
81.0 bp
10 bp - 100 bp
571
41.1 kb
108
8.2 kb
100 bp - 1 kb
3,734
1.5 Mb
1,637
844.8 kb
1 kb - 10 kb
729
1.1 Mb
1,009
1.8 Mb
10 kb - 100 kb
3
35.4 kb