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Dog vs Panda LastZ alignments

Dog (Canis lupus familiaris, CanFam3.1) and Panda (Ailuropoda melanoleuca, ailMel1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 68. Dog 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)
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

Dog Panda
Chunk size 30,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}

Results

Number of alignment blocks: 1,756,681

Genome coverage (bp) Coding exon coverage (bp)
Canis lupus familiaris

Uncovered: 449,782,780 out of 2,410,960,148
Covered: 1,961,177,368 out of 2,410,960,148

Uncovered: 544,021 out of 33,014,761
Matches: 29,973,791 out of 33,014,761
Mismatches: 2,339,845 out of 33,014,761
Insertions: 157,104 out of 33,014,761

Ailuropoda melanoleuca

Uncovered: 382,167,578 out of 2,299,492,210
Covered: 1,917,324,632 out of 2,299,492,210

Uncovered: 767,801 out of 31,130,938
Matches: 28,218,674 out of 31,130,938
Mismatches: 2,043,553 out of 31,130,938
Insertions: 100,910 out of 31,130,938