In this section

Fusarium verticillioides vs Trichoderma virens LastZ results

Fusarium verticillioides (Fusarium verticillioides 7600, ASM14955v1) and Trichoderma virens (Trichoderma virens Gv29-8, ASM17099v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Fusarium verticillioides 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 verticillioidesTrichoderma virens
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 20,423 alignment blocks

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

Uncovered: 27,465,619 out of 41,885,085
Covered: 14,419,466 out of 41,885,085

Uncovered: 6,428,723 out of 17,841,847
Matches: 7,547,442 out of 17,841,847
Mismatches: 3,578,487 out of 17,841,847
Insertions: 287,195 out of 17,841,847
Identity over aligned base-pairs: 66.1%

Trichoderma virens

Uncovered: 24,513,071 out of 39,022,666
Covered: 14,509,595 out of 39,022,666

Uncovered: 5,241,586 out of 17,541,951
Matches: 8,076,161 out of 17,541,951
Mismatches: 3,889,428 out of 17,541,951
Insertions: 334,776 out of 17,541,951
Identity over aligned base-pairs: 65.7%

Block size distribution

Size range All 20,423 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
31
196.0 bp
10 bp - 100 bp
1,877
124.0 kb
411
28.3 kb
100 bp - 1 kb
12,378
5.4 Mb
3,167
1.5 Mb
1 kb - 10 kb
6,135
11.2 Mb
2,967
6.5 Mb
10 kb - 100 kb
2
24.5 kb
231
6.5 Mb
100 kb - 1 Mb
16
2.2 Mb