In this section

Fusarium solani vs Trichoderma virens LastZ results

Fusarium solani (Fusarium solani mpVI 77-13-4, v2.0) and Trichoderma virens (Trichoderma virens Gv29-8, ASM17099v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Fusarium solani 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 solaniTrichoderma virens
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 23,661 alignment blocks

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

Uncovered: 34,510,882 out of 51,291,997
Covered: 16,781,115 out of 51,291,997

Uncovered: 9,106,137 out of 22,633,081
Matches: 8,972,043 out of 22,633,081
Mismatches: 4,212,235 out of 22,633,081
Insertions: 342,666 out of 22,633,081
Identity over aligned base-pairs: 66.3%

Trichoderma virens

Uncovered: 23,672,135 out of 39,022,666
Covered: 15,350,531 out of 39,022,666

Uncovered: 4,784,044 out of 17,541,951
Matches: 8,480,560 out of 17,541,951
Mismatches: 3,935,301 out of 17,541,951
Insertions: 342,046 out of 17,541,951
Identity over aligned base-pairs: 66.5%

Block size distribution

Size range All 23,661 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
29
148.0 bp
10 bp - 100 bp
2,161
142.4 kb
498
34.2 kb
100 bp - 1 kb
14,466
6.3 Mb
4,174
2.0 Mb
1 kb - 10 kb
7,000
13.0 Mb
3,698
8.0 Mb
10 kb - 100 kb
5
72.9 kb
201
6.0 Mb
100 kb - 1 Mb
20
3.4 Mb