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Ashbya gossypii vs Saccharomyces cerevisiae LastZ results

Ashbya gossypii (Ashbya gossypii ATCC 10895, ASM9102v1) and Saccharomyces cerevisiae (Saccharomyces cerevisiae S288c, R64-1-1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 94. 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 gossypiiSaccharomyces cerevisiae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 3,864 alignment blocks

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

Uncovered: 6,976,144 out of 9,119,312
Covered: 2,143,168 out of 9,119,312

Uncovered: 4,935,917 out of 7,019,450
Matches: 1,293,525 out of 7,019,450
Mismatches: 748,499 out of 7,019,450
Insertions: 41,509 out of 7,019,450
Identity over aligned base-pairs: 62.1%

Saccharomyces cerevisiae

Uncovered: 9,605,193 out of 12,157,105
Covered: 2,551,912 out of 12,157,105

Uncovered: 6,128,492 out of 8,596,583
Matches: 1,513,207 out of 8,596,583
Mismatches: 876,282 out of 8,596,583
Insertions: 78,602 out of 8,596,583
Identity over aligned base-pairs: 61.3%

Block size distribution

Size range All 3,864 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
23
85.0 bp
10 bp - 100 bp
517
35.7 kb
164
13.0 kb
100 bp - 1 kb
2,422
1.0 Mb
406
159.2 kb
1 kb - 10 kb
902
1.6 Mb
385
1.3 Mb
10 kb - 100 kb
68
1.2 Mb