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Fusarium oxysporum vs Magnaporthe oryzae LastZ results

Fusarium oxysporum (Fusarium oxysporum f. sp. lycopersici, FO2) and Magnaporthe oryzae (Magnaporthe oryzae 70-15, MG8) 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 oxysporumMagnaporthe oryzae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 25,383 alignment blocks

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

Uncovered: 47,591,278 out of 61,470,697
Covered: 13,879,419 out of 61,470,697

Uncovered: 10,933,336 out of 21,631,774
Matches: 6,833,835 out of 21,631,774
Mismatches: 3,569,650 out of 21,631,774
Insertions: 294,953 out of 21,631,774
Identity over aligned base-pairs: 63.9%

Magnaporthe oryzae

Uncovered: 26,994,455 out of 41,027,733
Covered: 14,033,278 out of 41,027,733

Uncovered: 6,625,117 out of 16,744,523
Matches: 6,168,052 out of 16,744,523
Mismatches: 3,527,559 out of 16,744,523
Insertions: 423,795 out of 16,744,523
Identity over aligned base-pairs: 61.0%

Block size distribution

Size range All 25,383 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
48
266.0 bp
10 bp - 100 bp
2,519
167.3 kb
539
36.1 kb
100 bp - 1 kb
16,849
6.9 Mb
4,897
2.2 Mb
1 kb - 10 kb
5,906
10.5 Mb
5,551
13.4 Mb
10 kb - 100 kb
61
874.7 kb
194
2.9 Mb