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Medicago truncatula vs Prunus dulcis LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Prunus dulcis (Prunus dulcis, ALMONDv2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 112. 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 dulcis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 157,915 alignment blocks

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

Uncovered: 377,825,625 out of 429,196,467
Covered: 51,370,842 out of 429,196,467

Uncovered: 14,739,744 out of 45,081,035
Matches: 21,386,344 out of 45,081,035
Mismatches: 8,367,451 out of 45,081,035
Insertions: 587,496 out of 45,081,035
Identity over aligned base-pairs: 70.5%

Prunus dulcis

Uncovered: 187,128,013 out of 227,498,357
Covered: 40,370,344 out of 227,498,357

Uncovered: 10,687,016 out of 33,980,404
Matches: 16,417,083 out of 33,980,404
Mismatches: 6,268,672 out of 33,980,404
Insertions: 607,633 out of 33,980,404
Identity over aligned base-pairs: 70.5%

Block size distribution

Size range All 157,915 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,397
7.6 kb
10 bp - 100 bp
22,149
1.4 Mb
5,685
410.1 kb
100 bp - 1 kb
121,518
42.8 Mb
32,346
11.6 Mb
1 kb - 10 kb
12,843
19.8 Mb
14,146
34.4 Mb
10 kb - 100 kb
8
141.6 kb
575
13.9 Mb
100 kb - 1 Mb
22
4.0 Mb