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Human vs Microbat LastZ alignments

Human (Homo sapiens, GRCh37) and Microbat (Myotis lucifugus, Myoluc2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 63. Human 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) 2200
Threshold for alignments between gapped alignment blocks (H) 2000
Masking count (M) 50
Seed and Transition value (T) 1
Scoring matrix (Q) Default

Results

Number of alignment blocks: 1815112

Genome coverage(bp) Coding exon coverage (bp)
Human
1,200,332,193 out of 3,098,825,702 32,721,373 out of 35,483,623
Microbat
1,117,054,385 out of 2,034,575,300 27,544,809 out of 30,512,546