Saccharomyces cerevisiae vs Ashbya gossypii LastZ results

Saccharomyces cerevisiae (Saccharomyces cerevisiae S288c, R64-1-1) and Ashbya gossypii (Ashbya gossypii ATCC 10895, ASM9102v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 67. Saccharomyces cerevisiae 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)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Statistics over 6,357 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Saccharomyces cerevisiae

Uncovered: 7,581,686 out of 12,157,105
Covered: 4,575,419 out of 12,157,105

Uncovered: 4,384,551 out of 8,832,031
Matches: 2,731,279 out of 8,832,031
Mismatches: 1,569,239 out of 8,832,031
Insertions: 146,962 out of 8,832,031
Identity over aligned base-pairs: 61.4%

Ashbya gossypii

Uncovered: 4,573,811 out of 9,119,312
Covered: 4,545,501 out of 9,119,312

Uncovered: 2,594,633 out of 7,019,450
Matches: 2,752,064 out of 7,019,450
Mismatches: 1,581,747 out of 7,019,450
Insertions: 91,006 out of 7,019,450
Identity over aligned base-pairs: 62.2%

Block size distribution

Size range All 6,357 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
124
470.0 bp
10 bp - 100 bp
1,436
91.0 kb
180
12.4 kb
100 bp - 1 kb
7,852
3.5 Mb
508
194.0 kb
1 kb - 10 kb
3,300
5.8 Mb
1,022
4.0 Mb
10 kb - 100 kb
2
22.5 kb
286
5.2 Mb