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Saccharomyces cerevisiae vs Schizosaccharomyces japonicus LastZ results

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288c, R64-1-1) and Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) 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 japonicus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,724 alignment blocks

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

Uncovered: 10,149,743 out of 12,157,105
Covered: 2,007,362 out of 12,157,105

Uncovered: 6,617,097 out of 8,596,583
Matches: 1,190,231 out of 8,596,583
Mismatches: 720,825 out of 8,596,583
Insertions: 68,430 out of 8,596,583
Identity over aligned base-pairs: 60.1%

Schizosaccharomyces japonicus

Uncovered: 9,857,004 out of 11,733,154
Covered: 1,876,150 out of 11,733,154

Uncovered: 5,045,890 out of 6,846,208
Matches: 1,093,899 out of 6,846,208
Mismatches: 657,247 out of 6,846,208
Insertions: 49,172 out of 6,846,208
Identity over aligned base-pairs: 60.8%

Block size distribution

Size range All 3,724 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3
12.0 bp
10 bp - 100 bp
358
24.4 kb
123
8.8 kb
100 bp - 1 kb
2,601
1.1 Mb
1,430
765.3 kb
1 kb - 10 kb
762
1.2 Mb
902
1.6 Mb
10 kb - 100 kb
1
11.9 kb