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Schizosaccharomyces japonicus vs Schizosaccharomyces pombe LastZ results

Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) and Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 94. Schizosaccharomyces japonicus 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 japonicusSchizosaccharomyces pombe
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,866 alignment blocks

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

Uncovered: 6,259,837 out of 11,733,154
Covered: 5,473,317 out of 11,733,154

Uncovered: 1,935,552 out of 6,846,208
Matches: 3,119,784 out of 6,846,208
Mismatches: 1,665,249 out of 6,846,208
Insertions: 125,623 out of 6,846,208
Identity over aligned base-pairs: 63.5%

Schizosaccharomyces pombe

Uncovered: 7,152,662 out of 12,631,379
Covered: 5,478,717 out of 12,631,379

Uncovered: 2,207,549 out of 7,176,702
Matches: 3,145,758 out of 7,176,702
Mismatches: 1,691,962 out of 7,176,702
Insertions: 131,433 out of 7,176,702
Identity over aligned base-pairs: 63.3%

Block size distribution

Size range All 7,866 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
12
60.0 bp
10 bp - 100 bp
894
61.6 kb
232
17.5 kb
100 bp - 1 kb
4,893
2.1 Mb
660
219.5 kb
1 kb - 10 kb
2,067
3.7 Mb
615
2.2 Mb
10 kb - 100 kb
173
3.3 Mb
100 kb - 1 Mb
1
105.1 kb