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
Parameter | Value |
---|---|
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 |
Uncovered: 4,384,551 out of 8,832,031 |
Ashbya gossypii |
Uncovered: 4,573,811 out of 9,119,312 |
Uncovered: 2,594,633 out of 7,019,450 |
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 |