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Chicken vs Turkey LastZ alignments

Chicken (Gallus gallus, WASHUC2) and Turkey (Meleagris gallopavo, UMD2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 61. Chicken 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

Results

Number of alignment blocks: 455970

Genome coverage(bp) Coding exon coverage (bp)
Chicken
942,910,163 out of 1,100,480,441 23,466,332 out of 24,644,731
Turkey
875,520,119 out of 1,061,982,190 21,944,292 out of 22,787,503