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Ashbya gossypii vs Schizosaccharomyces japonicus LastZ results

Ashbya gossypii (Ashbya gossypii ATCC 10895, ASM9102v1) and Schizosaccharomyces japonicus (Schizosaccharomyces japonicus yFS275, GCA_000149845.2) 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 japonicus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,641 alignment blocks

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

Uncovered: 8,387,515 out of 9,119,312
Covered: 731,797 out of 9,119,312

Uncovered: 6,292,551 out of 7,019,450
Matches: 437,395 out of 7,019,450
Mismatches: 264,885 out of 7,019,450
Insertions: 24,619 out of 7,019,450
Identity over aligned base-pairs: 60.2%

Schizosaccharomyces japonicus

Uncovered: 10,843,446 out of 11,733,154
Covered: 889,708 out of 11,733,154

Uncovered: 5,983,512 out of 6,846,208
Matches: 523,784 out of 6,846,208
Mismatches: 315,415 out of 6,846,208
Insertions: 23,497 out of 6,846,208
Identity over aligned base-pairs: 60.7%

Block size distribution

Size range All 1,641 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1
2.0 bp
10 bp - 100 bp
192
13.5 kb
69
5.3 kb
100 bp - 1 kb
1,177
503.1 kb
673
353.9 kb
1 kb - 10 kb
271
442.6 kb
348
600.0 kb