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Fusarium solani vs Saccharomyces cerevisiae LastZ results

Fusarium solani (Fusarium solani mpVI 77-13-4, v2.0) and Saccharomyces cerevisiae (Saccharomyces cerevisiae S288c, R64-1-1) 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 solaniSaccharomyces cerevisiae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,157 alignment blocks

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

Uncovered: 49,111,333 out of 51,291,997
Covered: 2,180,664 out of 51,291,997

Uncovered: 20,575,071 out of 22,633,081
Matches: 1,204,604 out of 22,633,081
Mismatches: 779,677 out of 22,633,081
Insertions: 73,729 out of 22,633,081
Identity over aligned base-pairs: 58.5%

Saccharomyces cerevisiae

Uncovered: 10,155,462 out of 12,157,105
Covered: 2,001,643 out of 12,157,105

Uncovered: 6,615,390 out of 8,596,583
Matches: 1,179,585 out of 8,596,583
Mismatches: 747,118 out of 8,596,583
Insertions: 54,490 out of 8,596,583
Identity over aligned base-pairs: 59.5%

Block size distribution

Size range All 5,157 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
13
81.0 bp
10 bp - 100 bp
608
42.9 kb
124
9.7 kb
100 bp - 1 kb
3,821
1.5 Mb
1,589
800.1 kb
1 kb - 10 kb
715
1.1 Mb
1,060
1.8 Mb