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Fusarium oxysporum vs Trichoderma virens LastZ results

Fusarium oxysporum (Fusarium oxysporum f. sp. lycopersici, FO2) and Trichoderma virens (Trichoderma virens Gv29-8, ASM17099v1) 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 oxysporumTrichoderma virens
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 25,849 alignment blocks

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

Uncovered: 43,657,725 out of 61,470,697
Covered: 17,812,972 out of 61,470,697

Uncovered: 8,761,669 out of 21,631,774
Matches: 8,452,501 out of 21,631,774
Mismatches: 4,093,431 out of 21,631,774
Insertions: 324,173 out of 21,631,774
Identity over aligned base-pairs: 65.7%

Trichoderma virens

Uncovered: 24,289,006 out of 39,022,666
Covered: 14,733,660 out of 39,022,666

Uncovered: 5,108,324 out of 17,541,951
Matches: 8,108,513 out of 17,541,951
Mismatches: 3,986,748 out of 17,541,951
Insertions: 338,366 out of 17,541,951
Identity over aligned base-pairs: 65.2%

Block size distribution

Size range All 25,849 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
62
367.0 bp
10 bp - 100 bp
2,397
159.5 kb
699
48.1 kb
100 bp - 1 kb
16,041
6.9 Mb
5,130
2.4 Mb
1 kb - 10 kb
7,344
13.2 Mb
4,312
9.1 Mb
10 kb - 100 kb
5
81.7 kb
233
6.6 Mb
100 kb - 1 Mb
15
2.2 Mb