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Stickleback vs Cod LastZ alignments

Stickleback (Gasterosteus aculeatus, BROADS1) and Cod (Gadus morhua, gadMor1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 64. Stickleback 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) 5000
Threshold for alignments between gapped alignment blocks (H) 3000
Masking count (M) 50
Seed and Transition value (T) 1
Scoring matrix (Q) Default

Results

Number of alignment blocks: 300871

Genome coverage(bp) Coding exon coverage (bp)
Stickleback
81,103,068 out of 461,533,448 28,382,247 out of 32,649,418
Cod
74,852,387 out of 832,114,588 24,999,993 out of 29,438,356