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Ashbya gossypii vs Schizosaccharomyces octosporus LastZ results

Ashbya gossypii (Ashbya gossypii ATCC 10895, ASM9102v1) and Schizosaccharomyces octosporus (Schizosaccharomyces octosporus yFS286, GCA_000150505.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Ashbya gossypii 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

ParameterAshbya gossypiiSchizosaccharomyces octosporus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,498 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Ashbya gossypii

Uncovered: 8,426,689 out of 9,119,312
Covered: 692,623 out of 9,119,312

Uncovered: 6,333,064 out of 7,019,450
Matches: 408,606 out of 7,019,450
Mismatches: 256,626 out of 7,019,450
Insertions: 21,154 out of 7,019,450
Identity over aligned base-pairs: 59.5%

Schizosaccharomyces octosporus

Uncovered: 10,803,304 out of 11,634,473
Covered: 831,169 out of 11,634,473

Uncovered: 6,108,998 out of 6,921,651
Matches: 486,808 out of 6,921,651
Mismatches: 304,713 out of 6,921,651
Insertions: 21,132 out of 6,921,651
Identity over aligned base-pairs: 59.9%

Block size distribution

Size range All 1,498 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2
11.0 bp
10 bp - 100 bp
159
11.9 kb
71
5.8 kb
100 bp - 1 kb
1,085
458.5 kb
631
324.0 kb
1 kb - 10 kb
252
423.0 kb
324
563.6 kb