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Schizosaccharomyces japonicus vs Trichoderma virens LastZ results

Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) and Trichoderma virens (Trichoderma virens Gv29-8, ASM17099v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Schizosaccharomyces japonicus 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

ParameterSchizosaccharomyces japonicusTrichoderma virens
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,337 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Schizosaccharomyces japonicus

Uncovered: 9,529,215 out of 11,733,154
Covered: 2,203,939 out of 11,733,154

Uncovered: 4,730,137 out of 6,846,208
Matches: 1,301,207 out of 6,846,208
Mismatches: 764,322 out of 6,846,208
Insertions: 50,542 out of 6,846,208
Identity over aligned base-pairs: 61.5%

Trichoderma virens

Uncovered: 36,735,654 out of 39,022,666
Covered: 2,287,012 out of 39,022,666

Uncovered: 15,370,095 out of 17,541,951
Matches: 1,303,592 out of 17,541,951
Mismatches: 779,162 out of 17,541,951
Insertions: 89,102 out of 17,541,951
Identity over aligned base-pairs: 60.0%

Block size distribution

Size range All 5,337 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4
23.0 bp
10 bp - 100 bp
733
51.0 kb
91
6.6 kb
100 bp - 1 kb
3,927
1.5 Mb
1,496
826.9 kb
1 kb - 10 kb
673
1.1 Mb
1,019
1.8 Mb
10 kb - 100 kb
2
44.0 kb