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Chicken vs Zebra Finch LastZ alignments

Chicken (Gallus gallus, Galgal4) and Zebra Finch (Taeniopygia guttata, taeGut3.2.4) 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)50
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

Chicken Zebra Finch
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}

Results

Number of alignment blocks: 815,468

Genome coverage (bp) Coding exon coverage (bp)
Gallus gallus

Uncovered: 294,921,805 out of 1,046,932,099
Covered: 752,010,294 out of 1,046,932,099

Uncovered: 1,707,889 out of 25,934,237
Matches: 20,810,574 out of 25,934,237
Mismatches: 3,245,599 out of 25,934,237
Insertions: 170,175 out of 25,934,237

Taeniopygia guttata

Uncovered: 499,219,144 out of 1,233,186,341
Covered: 733,967,197 out of 1,233,186,341

Uncovered: 2,575,396 out of 23,643,636
Matches: 18,445,003 out of 23,643,636
Mismatches: 2,542,393 out of 23,643,636
Insertions: 80,844 out of 23,643,636