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Schizosaccharomyces japonicus vs Schizosaccharomyces octosporus LastZ results

Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) and Schizosaccharomyces octosporus (Schizosaccharomyces octosporus yFS286, GCA_000150505.2) 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 octosporus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,051 alignment blocks

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

Uncovered: 6,257,743 out of 11,733,154
Covered: 5,475,411 out of 11,733,154

Uncovered: 1,986,696 out of 6,846,208
Matches: 3,075,801 out of 6,846,208
Mismatches: 1,653,772 out of 6,846,208
Insertions: 129,939 out of 6,846,208
Identity over aligned base-pairs: 63.3%

Schizosaccharomyces octosporus

Uncovered: 6,196,665 out of 11,634,473
Covered: 5,437,808 out of 11,634,473

Uncovered: 2,050,274 out of 6,921,651
Matches: 3,073,458 out of 6,921,651
Mismatches: 1,666,425 out of 6,921,651
Insertions: 131,494 out of 6,921,651
Identity over aligned base-pairs: 63.1%

Block size distribution

Size range All 8,051 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
23
141.0 bp
10 bp - 100 bp
964
66.7 kb
255
18.9 kb
100 bp - 1 kb
4,991
2.1 Mb
816
253.6 kb
1 kb - 10 kb
2,073
3.7 Mb
588
2.2 Mb
10 kb - 100 kb
179
3.4 Mb