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Schizosaccharomyces octosporus vs Schizosaccharomyces pombe LastZ results

Schizosaccharomyces octosporus (Schizosaccharomyces octosporus yFS286, GCA_000150505.2) and Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 94. Schizosaccharomyces octosporus 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 octosporusSchizosaccharomyces pombe
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 7,288 alignment blocks

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

Uncovered: 3,919,062 out of 11,634,473
Covered: 7,715,411 out of 11,634,473

Uncovered: 614,062 out of 6,921,651
Matches: 4,198,661 out of 6,921,651
Mismatches: 1,976,652 out of 6,921,651
Insertions: 132,276 out of 6,921,651
Identity over aligned base-pairs: 66.6%

Schizosaccharomyces pombe

Uncovered: 4,815,114 out of 12,631,379
Covered: 7,816,265 out of 12,631,379

Uncovered: 817,380 out of 7,176,702
Matches: 4,223,334 out of 7,176,702
Mismatches: 1,990,694 out of 7,176,702
Insertions: 145,294 out of 7,176,702
Identity over aligned base-pairs: 66.4%

Block size distribution

Size range All 7,288 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15
113.0 bp
10 bp - 100 bp
709
45.2 kb
246
15.5 kb
100 bp - 1 kb
3,598
1.6 Mb
499
152.0 kb
1 kb - 10 kb
2,963
6.6 Mb
196
470.9 kb
10 kb - 100 kb
3
38.6 kb
56
2.0 Mb
100 kb - 1 Mb
20
5.7 Mb