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C.intestinalis vs C.savignyi LastZ alignments

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 are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Configuration parameters

ParameterValue
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

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}

Results

Number of alignment blocks: 122,740

Genome coverage (bp) Coding exon coverage (bp)
Ciona intestinalis

Uncovered: 78,727,133 out of 115,212,710
Covered: 36,485,577 out of 115,212,710

Uncovered: 2,479,964 out of 16,105,584
Matches: 9,708,995 out of 16,105,584
Mismatches: 3,748,605 out of 16,105,584
Insertions: 168,020 out of 16,105,584

Ciona savignyi

Uncovered: 142,454,747 out of 176,989,013
Covered: 34,534,266 out of 176,989,013

Uncovered: 2,714,820 out of 13,806,906
Matches: 7,987,391 out of 13,806,906
Mismatches: 2,979,814 out of 13,806,906
Insertions: 124,881 out of 13,806,906