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Ashbya gossypii vs Schizosaccharomyces cryophilus LastZ results

Ashbya gossypii (Ashbya gossypii ATCC 10895, ASM9102v1) and Schizosaccharomyces cryophilus (Schizosaccharomyces cryophilus OY26, GCA_000004155.2) 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 cryophilus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,508 alignment blocks

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

Uncovered: 8,428,412 out of 9,119,312
Covered: 690,900 out of 9,119,312

Uncovered: 6,335,507 out of 7,019,450
Matches: 407,424 out of 7,019,450
Mismatches: 255,579 out of 7,019,450
Insertions: 20,940 out of 7,019,450
Identity over aligned base-pairs: 59.6%

Schizosaccharomyces cryophilus

Uncovered: 10,714,179 out of 11,554,764
Covered: 840,585 out of 11,554,764

Uncovered: 6,184,825 out of 7,004,290
Matches: 490,803 out of 7,004,290
Mismatches: 306,778 out of 7,004,290
Insertions: 21,884 out of 7,004,290
Identity over aligned base-pairs: 59.9%

Block size distribution

Size range All 1,508 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1
7.0 bp
10 bp - 100 bp
160
11.8 kb
73
6.1 kb
100 bp - 1 kb
1,086
469.2 kb
629
336.2 kb
1 kb - 10 kb
261
422.1 kb
316
560.8 kb