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Magnaporthe oryzae vs Trichoderma virens LastZ results

Magnaporthe oryzae (Magnaporthe oryzae 70-15, MG8) and Trichoderma virens (Trichoderma virens Gv29-8, ASM17099v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Magnaporthe oryzae 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

ParameterMagnaporthe oryzaeTrichoderma virens
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 18,814 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Magnaporthe oryzae

Uncovered: 30,270,005 out of 41,027,733
Covered: 10,757,728 out of 41,027,733

Uncovered: 7,347,679 out of 16,744,523
Matches: 5,969,687 out of 16,744,523
Mismatches: 3,023,396 out of 16,744,523
Insertions: 403,761 out of 16,744,523
Identity over aligned base-pairs: 63.5%

Trichoderma virens

Uncovered: 28,434,453 out of 39,022,666
Covered: 10,588,213 out of 39,022,666

Uncovered: 7,991,064 out of 17,541,951
Matches: 6,140,224 out of 17,541,951
Mismatches: 3,140,151 out of 17,541,951
Insertions: 270,512 out of 17,541,951
Identity over aligned base-pairs: 64.3%

Block size distribution

Size range All 18,814 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
35
194.0 bp
10 bp - 100 bp
1,970
131.2 kb
269
18.5 kb
100 bp - 1 kb
12,716
5.3 Mb
2,891
1.4 Mb
1 kb - 10 kb
4,091
6.9 Mb
3,718
9.4 Mb
10 kb - 100 kb
2
24.9 kb
103
1.5 Mb