C.intestinalis vs C.savignyi LastZ results
C.intestinalis (Ciona intestinalis, KH) and C.savignyi (Ciona savignyi, CSAV2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 66. 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) | 50 |
| 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 | C.savignyi |
|---|---|---|
| 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 122,740 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| C.intestinalis |
Uncovered: 78,727,133 out of 115,212,710 |
Uncovered: 2,479,964 out of 16,105,584 |
| C.savignyi |
Uncovered: 142,454,747 out of 176,989,013 |
Uncovered: 2,714,820 out of 13,806,906 |
Block size distribution
| Size range | All 122,740 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 606 |
3.6 kb |
|||
| 10 bp - 100 bp | 13,890 |
934.3 kb |
1,452 |
102.3 kb |
|
| 100 bp - 1 kb | 102,590 |
29.3 Mb |
7,063 |
2.5 Mb |
|
| 1 kb - 10 kb | 5,646 |
8.8 Mb |
4,619 |
15.1 Mb |
|
| 10 kb - 100 kb | 8 |
107.9 kb |
943 |
20.1 Mb |
|
| 100 kb - 1 Mb | 9 |
1.4 Mb |
|||