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Medicago truncatula vs Prunus avium LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Prunus avium (Prunus avium, PAV_r1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Medicago truncatula 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.

Results

Number of alignment blocks: 196,769

Genome coverage (bp) Coding exon coverage (bp)
Medicago truncatula

Uncovered: 353,089,020 out of 412,800,391
Covered: 59,711,371 out of 412,800,391

Uncovered: 14,838,093 out of 50,132,764
Matches: 24,510,511 out of 50,132,764
Mismatches: 10,077,154 out of 50,132,764
Insertions: 707,006 out of 50,132,764

Prunus avium

Uncovered: 219,414,454 out of 272,361,615
Covered: 52,947,161 out of 272,361,615

Uncovered: 13,579,498 out of 38,693,511
Matches: 17,245,263 out of 38,693,511
Mismatches: 7,162,055 out of 38,693,511
Insertions: 706,695 out of 38,693,511

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
Other parameters (other)--ambiguous=iupac

Chunking parameters

Medicago truncatula Prunus avium
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}