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Chicken vs Anole lizard LastZ Results

Chicken (Gallus gallus, Galgal4) and Anole lizard (Anolis carolinensis, AnoCar2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 71. 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.

Configuration parameters

ParameterValue
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)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterChickenAnole lizard
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 266,363 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Chicken

Uncovered: 968,589,363 out of 1,046,932,099
Covered: 78,342,736 out of 1,046,932,099

Uncovered: 3,574,630 out of 25,934,237
Matches: 16,961,817 out of 25,934,237
Mismatches: 5,195,244 out of 25,934,237
Insertions: 202,546 out of 25,934,237

Anole lizard

Uncovered: 1,724,782,357 out of 1,799,143,587
Covered: 74,361,230 out of 1,799,143,587

Uncovered: 8,412,745 out of 29,512,185
Matches: 16,042,643 out of 29,512,185
Mismatches: 4,848,759 out of 29,512,185
Insertions: 208,038 out of 29,512,185