In this section

Schizosaccharomyces cryophilus vs Schizosaccharomyces octosporus LastZ results

Schizosaccharomyces cryophilus (Schizosaccharomyces cryophilus OY26, GCA_000004155.2) and Schizosaccharomyces octosporus (Schizosaccharomyces octosporus yFS286, GCA_000150505.2) 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 octosporus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,667 alignment blocks

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

Uncovered: 1,012,847 out of 11,554,764
Covered: 10,541,917 out of 11,554,764

Uncovered: 80,814 out of 7,004,290
Matches: 5,528,439 out of 7,004,290
Mismatches: 1,363,715 out of 7,004,290
Insertions: 31,322 out of 7,004,290
Identity over aligned base-pairs: 79.9%

Schizosaccharomyces octosporus

Uncovered: 1,011,426 out of 11,634,473
Covered: 10,623,047 out of 11,634,473

Uncovered: 29,898 out of 6,921,651
Matches: 5,566,260 out of 6,921,651
Mismatches: 1,293,812 out of 6,921,651
Insertions: 31,681 out of 6,921,651
Identity over aligned base-pairs: 80.8%

Block size distribution

Size range All 3,667 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
38
200.0 bp
10 bp - 100 bp
572
34.7 kb
281
18.6 kb
100 bp - 1 kb
1,542
547.6 kb
570
190.1 kb
1 kb - 10 kb
1,153
4.4 Mb
241
515.9 kb
10 kb - 100 kb
361
6.2 Mb
7
273.8 kb
100 kb - 1 Mb
1
120.1 kb
18
7.0 Mb
1 Mb - 10 Mb
3
3.3 Mb