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Saccharomyces cerevisiae vs Schizosaccharomyces pombe LastZ results

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288c, R64-1-1) and Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) 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 pombe
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,804 alignment blocks

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

Uncovered: 9,924,142 out of 12,157,105
Covered: 2,232,963 out of 12,157,105

Uncovered: 6,414,368 out of 8,596,583
Matches: 1,317,308 out of 8,596,583
Mismatches: 780,014 out of 8,596,583
Insertions: 84,893 out of 8,596,583
Identity over aligned base-pairs: 60.4%

Schizosaccharomyces pombe

Uncovered: 10,583,142 out of 12,631,379
Covered: 2,048,237 out of 12,631,379

Uncovered: 5,203,098 out of 7,176,702
Matches: 1,201,190 out of 7,176,702
Mismatches: 712,237 out of 7,176,702
Insertions: 60,177 out of 7,176,702
Identity over aligned base-pairs: 60.9%

Block size distribution

Size range All 3,804 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5
26.0 bp
10 bp - 100 bp
315
21.9 kb
123
9.2 kb
100 bp - 1 kb
2,642
1.2 Mb
1,509
811.4 kb
1 kb - 10 kb
842
1.4 Mb
998
1.8 Mb
10 kb - 100 kb
1
12.9 kb