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Medicago truncatula vs Prunus avium LastZ results

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 99. Medicago truncatula was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was 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

ParameterMedicago truncatulaPrunus avium
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 181,351 alignment blocks

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

Uncovered: 355,588,823 out of 412,800,391
Covered: 57,211,568 out of 412,800,391

Uncovered: 15,207,929 out of 50,132,764
Matches: 24,395,191 out of 50,132,764
Mismatches: 9,836,315 out of 50,132,764
Insertions: 693,329 out of 50,132,764
Identity over aligned base-pairs: 69.9%

Prunus avium

Uncovered: 224,786,352 out of 272,361,615
Covered: 47,575,263 out of 272,361,615

Uncovered: 15,294,133 out of 38,693,511
Matches: 16,199,068 out of 38,693,511
Mismatches: 6,553,692 out of 38,693,511
Insertions: 646,618 out of 38,693,511
Identity over aligned base-pairs: 69.2%

Block size distribution

Size range All 181,351 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,695
9.1 kb
10 bp - 100 bp
25,518
1.6 Mb
6,642
480.7 kb
100 bp - 1 kb
138,783
48.9 Mb
38,909
14.2 Mb
1 kb - 10 kb
15,322
24.1 Mb
17,314
41.7 Mb
10 kb - 100 kb
33
858.3 kb
735
17.2 Mb
100 kb - 1 Mb
16
2.0 Mb