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Saccharomyces cerevisiae vs Schizosaccharomyces octosporus LastZ results

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288c, R64-1-1) and Schizosaccharomyces octosporus (Schizosaccharomyces octosporus yFS286, GCA_000150505.2) 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 octosporus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,787 alignment blocks

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

Uncovered: 9,984,542 out of 12,157,105
Covered: 2,172,563 out of 12,157,105

Uncovered: 6,469,108 out of 8,596,583
Matches: 1,284,643 out of 8,596,583
Mismatches: 761,225 out of 8,596,583
Insertions: 81,607 out of 8,596,583
Identity over aligned base-pairs: 60.4%

Schizosaccharomyces octosporus

Uncovered: 9,638,795 out of 11,634,473
Covered: 1,995,678 out of 11,634,473

Uncovered: 5,002,035 out of 6,921,651
Matches: 1,168,883 out of 6,921,651
Mismatches: 693,598 out of 6,921,651
Insertions: 57,135 out of 6,921,651
Identity over aligned base-pairs: 60.9%

Block size distribution

Size range All 3,787 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2
10.0 bp
10 bp - 100 bp
376
26.7 kb
138
10.0 kb
100 bp - 1 kb
2,599
1.2 Mb
1,515
795.3 kb
1 kb - 10 kb
810
1.3 Mb
967
1.7 Mb
10 kb - 100 kb
1
12.3 kb