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Fusarium oxysporum vs Saccharomyces cerevisiae LastZ results

Fusarium oxysporum (Fusarium oxysporum f. sp. lycopersici, FO2) and Saccharomyces cerevisiae (Saccharomyces cerevisiae S288c, R64-1-1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Fusarium oxysporum 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 oxysporumSaccharomyces cerevisiae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,335 alignment blocks

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

Uncovered: 59,004,526 out of 61,470,697
Covered: 2,466,171 out of 61,470,697

Uncovered: 19,588,870 out of 21,631,774
Matches: 1,202,229 out of 21,631,774
Mismatches: 762,701 out of 21,631,774
Insertions: 77,974 out of 21,631,774
Identity over aligned base-pairs: 58.8%

Saccharomyces cerevisiae

Uncovered: 10,009,348 out of 12,157,105
Covered: 2,147,757 out of 12,157,105

Uncovered: 6,516,054 out of 8,596,583
Matches: 1,229,098 out of 8,596,583
Mismatches: 791,712 out of 8,596,583
Insertions: 59,719 out of 8,596,583
Identity over aligned base-pairs: 59.1%

Block size distribution

Size range All 5,335 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9
46.0 bp
10 bp - 100 bp
618
43.6 kb
138
10.3 kb
100 bp - 1 kb
3,877
1.5 Mb
1,746
880.5 kb
1 kb - 10 kb
828
1.3 Mb
1,089
1.9 Mb
10 kb - 100 kb
3
74.9 kb
5
109.2 kb