C.intestinalis vs C.intestinalis LastZ results
C.intestinalis (Ciona intestinalis, KH) and C.intestinalis (Ciona intestinalis, KH) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 82. C.intestinalis 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) | 400 |
| Gap extend penalty (E) | 30 |
| HSP threshold (K) | 3000 |
| 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
| Parameter | C.intestinalis (reference) | C.intestinalis (non-reference) |
|---|---|---|
| Chunk size | 10,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 0 | 10,100,000 |
| Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 22,838 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| C.intestinalis |
Uncovered: 882,568,693 out of 885,550,958 |
Uncovered: 10,266,067 out of 12,541,363 |