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Fusarium oxysporum vs Schizosaccharomyces pombe LastZ results

Fusarium oxysporum (Fusarium oxysporum f. sp. lycopersici, FO2) and Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) 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 pombe
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,671 alignment blocks

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

Uncovered: 58,727,716 out of 61,470,697
Covered: 2,742,981 out of 61,470,697

Uncovered: 19,343,566 out of 21,631,774
Matches: 1,350,833 out of 21,631,774
Mismatches: 846,255 out of 21,631,774
Insertions: 91,120 out of 21,631,774
Identity over aligned base-pairs: 59.0%

Schizosaccharomyces pombe

Uncovered: 10,378,220 out of 12,631,379
Covered: 2,253,159 out of 12,631,379

Uncovered: 5,045,979 out of 7,176,702
Matches: 1,276,408 out of 7,176,702
Mismatches: 806,148 out of 7,176,702
Insertions: 48,167 out of 7,176,702
Identity over aligned base-pairs: 59.9%

Block size distribution

Size range All 5,671 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
10
64.0 bp
10 bp - 100 bp
678
47.7 kb
129
10.0 kb
100 bp - 1 kb
4,125
1.6 Mb
1,688
906.3 kb
1 kb - 10 kb
855
1.4 Mb
1,160
2.1 Mb
10 kb - 100 kb
3
85.7 kb
6
133.4 kb