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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.

Full list of pairwise alignments

Configuration parameters

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


Number of alignment blocks: 122740

Genome coverage(bp) Coding exon coverage (bp)
36,485,577 out of 115,212,710 13,625,889 out of 16,105,584
34,534,266 out of 176,989,013 11,092,442 out of 13,806,906