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Chicken vs Anole Lizard LastZ alignments

Chicken (Gallus gallus, WASHUC2) and Anole Lizard (Anolis carolinensis, AnoCar2.0) 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: 267654

Genome coverage(bp) Coding exon coverage (bp)
Chicken
77,677,283 out of 1,100,480,441 21,206,752 out of 24,644,731
Anole Lizard
72,765,433 out of 1,799,126,364 19,569,991 out of 27,358,934