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Schizosaccharomyces cryophilus vs Schizosaccharomyces pombe LastZ results

Schizosaccharomyces cryophilus (Schizosaccharomyces cryophilus OY26, GCA_000004155.2) and Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 94. Schizosaccharomyces cryophilus 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

ParameterSchizosaccharomyces cryophilusSchizosaccharomyces pombe
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,420 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Schizosaccharomyces cryophilus

Uncovered: 3,714,812 out of 11,554,764
Covered: 7,839,952 out of 11,554,764

Uncovered: 635,698 out of 7,004,290
Matches: 4,253,276 out of 7,004,290
Mismatches: 1,985,215 out of 7,004,290
Insertions: 130,101 out of 7,004,290
Identity over aligned base-pairs: 66.8%

Schizosaccharomyces pombe

Uncovered: 4,727,160 out of 12,631,379
Covered: 7,904,219 out of 12,631,379

Uncovered: 765,467 out of 7,176,702
Matches: 4,270,138 out of 7,176,702
Mismatches: 1,997,503 out of 7,176,702
Insertions: 143,594 out of 7,176,702
Identity over aligned base-pairs: 66.6%

Block size distribution

Size range All 7,420 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4
27.0 bp
10 bp - 100 bp
727
45.7 kb
233
14.6 kb
100 bp - 1 kb
3,698
1.6 Mb
596
194.2 kb
1 kb - 10 kb
2,985
6.7 Mb
229
517.5 kb
10 kb - 100 kb
6
73.6 kb
61
2.3 Mb
100 kb - 1 Mb
21
5.4 Mb