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Saccharomyces cerevisiae vs Schizosaccharomyces cryophilus LastZ results

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288c, R64-1-1) and Schizosaccharomyces cryophilus (Schizosaccharomyces cryophilus OY26, GCA_000004155.2) 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 cerevisiaeSchizosaccharomyces cryophilus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,858 alignment blocks

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

Uncovered: 10,001,287 out of 12,157,105
Covered: 2,155,818 out of 12,157,105

Uncovered: 6,479,773 out of 8,596,583
Matches: 1,279,207 out of 8,596,583
Mismatches: 759,198 out of 8,596,583
Insertions: 78,405 out of 8,596,583
Identity over aligned base-pairs: 60.4%

Schizosaccharomyces cryophilus

Uncovered: 9,579,773 out of 11,554,764
Covered: 1,974,991 out of 11,554,764

Uncovered: 5,094,285 out of 7,004,290
Matches: 1,162,894 out of 7,004,290
Mismatches: 689,454 out of 7,004,290
Insertions: 57,657 out of 7,004,290
Identity over aligned base-pairs: 60.9%

Block size distribution

Size range All 3,858 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2
12.0 bp
10 bp - 100 bp
392
28.1 kb
156
11.9 kb
100 bp - 1 kb
2,645
1.1 Mb
1,513
793.8 kb
1 kb - 10 kb
819
1.3 Mb
962
1.7 Mb