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Fusarium oxysporum vs Schizosaccharomyces octosporus LastZ results

Fusarium oxysporum (Fusarium oxysporum f. sp. lycopersici, FO2) and Schizosaccharomyces octosporus (Schizosaccharomyces octosporus yFS286, GCA_000150505.2) 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 oxysporumSchizosaccharomyces octosporus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,594 alignment blocks

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

Uncovered: 58,759,472 out of 61,470,697
Covered: 2,711,225 out of 61,470,697

Uncovered: 19,373,314 out of 21,631,774
Matches: 1,338,317 out of 21,631,774
Mismatches: 830,601 out of 21,631,774
Insertions: 89,542 out of 21,631,774
Identity over aligned base-pairs: 59.3%

Schizosaccharomyces octosporus

Uncovered: 9,413,688 out of 11,634,473
Covered: 2,220,785 out of 11,634,473

Uncovered: 4,828,354 out of 6,921,651
Matches: 1,249,479 out of 6,921,651
Mismatches: 795,344 out of 6,921,651
Insertions: 48,474 out of 6,921,651
Identity over aligned base-pairs: 59.7%

Block size distribution

Size range All 5,594 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7
43.0 bp
10 bp - 100 bp
755
51.8 kb
149
10.6 kb
100 bp - 1 kb
3,979
1.6 Mb
1,635
871.2 kb
1 kb - 10 kb
848
1.3 Mb
1,133
2.0 Mb
10 kb - 100 kb
5
120.9 kb
7
184.8 kb