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Apis mellifera vs Atta cephalotes LastZ Results

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Apis mellifera (Apis mellifera, Amel_4.5) and Atta cephalotes (Atta cephalotes, Attacep1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Apis mellifera 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.


Number of alignment blocks: 125,470

Genome coverage (bp) Coding exon coverage (bp)
Apis mellifera

Uncovered: 200,641,390 out of 250,270,657
Covered: 49,629,267 out of 250,270,657

Uncovered: 2,839,671 out of 19,369,619
Matches: 11,602,663 out of 19,369,619
Mismatches: 4,612,570 out of 19,369,619
Insertions: 314,715 out of 19,369,619

Atta cephalotes

Uncovered: 261,142,559 out of 317,690,795
Covered: 56,548,236 out of 317,690,795

Uncovered: 1,943,176 out of 17,986,937
Matches: 11,297,883 out of 17,986,937
Mismatches: 4,400,634 out of 17,986,937
Insertions: 345,244 out of 17,986,937

Configuration parameters

Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac

Chunking parameters

Apis mellifera Atta cephalotes
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}