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Saccharomyces cerevisiae vs Trichoderma virens LastZ results

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288c, R64-1-1) and Trichoderma virens (Trichoderma virens Gv29-8, ASM17099v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Saccharomyces cerevisiae 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

ParameterSaccharomyces cerevisiaeTrichoderma virens
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,788 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Saccharomyces cerevisiae

Uncovered: 10,155,707 out of 12,157,105
Covered: 2,001,398 out of 12,157,105

Uncovered: 6,621,749 out of 8,596,583
Matches: 1,181,048 out of 8,596,583
Mismatches: 740,183 out of 8,596,583
Insertions: 53,603 out of 8,596,583
Identity over aligned base-pairs: 59.8%

Trichoderma virens

Uncovered: 37,104,348 out of 39,022,666
Covered: 1,918,318 out of 39,022,666

Uncovered: 15,710,029 out of 17,541,951
Matches: 1,081,995 out of 17,541,951
Mismatches: 685,431 out of 17,541,951
Insertions: 64,496 out of 17,541,951
Identity over aligned base-pairs: 59.1%

Block size distribution

Size range All 4,788 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7
39.0 bp
10 bp - 100 bp
566
39.9 kb
80
5.6 kb
100 bp - 1 kb
3,614
1.4 Mb
1,443
750.4 kb
1 kb - 10 kb
601
931.8 kb
918
1.6 Mb
10 kb - 100 kb
2
21.7 kb