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Fusarium oxysporum vs Fusarium solani LastZ results

Fusarium oxysporum (Fusarium oxysporum f. sp. lycopersici, FO2) and Fusarium solani (Fusarium solani mpVI 77-13-4, v2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 94. 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 oxysporumFusarium solani
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 46,654 alignment blocks

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

Uncovered: 25,491,357 out of 61,470,697
Covered: 35,979,340 out of 61,470,697

Uncovered: 3,698,045 out of 21,631,774
Matches: 12,853,213 out of 21,631,774
Mismatches: 4,804,484 out of 21,631,774
Insertions: 276,032 out of 21,631,774
Identity over aligned base-pairs: 71.7%

Fusarium solani

Uncovered: 21,279,424 out of 51,291,997
Covered: 30,012,573 out of 51,291,997

Uncovered: 4,652,176 out of 22,633,081
Matches: 12,674,810 out of 22,633,081
Mismatches: 4,998,048 out of 22,633,081
Insertions: 308,047 out of 22,633,081
Identity over aligned base-pairs: 70.5%

Block size distribution

Size range All 46,654 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
204
1.1 kb
10 bp - 100 bp
5,702
369.0 kb
2,467
167.9 kb
100 bp - 1 kb
26,829
10.8 Mb
11,348
4.6 Mb
1 kb - 10 kb
13,861
30.7 Mb
7,441
17.1 Mb
10 kb - 100 kb
58
826.8 kb
214
5.0 Mb
100 kb - 1 Mb
34
11.8 Mb
1 Mb - 10 Mb
2
4.0 Mb