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Ashbya gossypii vs Schizosaccharomyces pombe LastZ results

Ashbya gossypii (Ashbya gossypii ATCC 10895, ASM9102v1) and Schizosaccharomyces pombe (Schizosaccharomyces pombe 972h-, ASM294v2) 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 pombe
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,423 alignment blocks

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

Uncovered: 8,436,299 out of 9,119,312
Covered: 683,013 out of 9,119,312

Uncovered: 6,342,164 out of 7,019,450
Matches: 402,677 out of 7,019,450
Mismatches: 253,336 out of 7,019,450
Insertions: 21,273 out of 7,019,450
Identity over aligned base-pairs: 59.5%

Schizosaccharomyces pombe

Uncovered: 11,814,246 out of 12,631,379
Covered: 817,133 out of 12,631,379

Uncovered: 6,370,921 out of 7,176,702
Matches: 482,618 out of 7,176,702
Mismatches: 302,113 out of 7,176,702
Insertions: 21,050 out of 7,176,702
Identity over aligned base-pairs: 59.9%

Block size distribution

Size range All 1,423 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
10 bp - 100 bp
111
8.2 kb
38
3.1 kb
100 bp - 1 kb
1,060
459.7 kb
600
317.9 kb
1 kb - 10 kb
252
412.4 kb
319
559.4 kb