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Medicago truncatula vs Prunus dulcis LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Prunus dulcis (Prunus dulcis, ALMONDv2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. 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 size010,100,000
Masking options

Statistics over 184,917 alignment blocks

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

Uncovered: 354,436,906 out of 412,800,391
Covered: 58,363,485 out of 412,800,391

Uncovered: 14,979,626 out of 50,132,764
Matches: 24,529,345 out of 50,132,764
Mismatches: 9,922,079 out of 50,132,764
Insertions: 701,714 out of 50,132,764
Identity over aligned base-pairs: 69.8%

Prunus dulcis

Uncovered: 178,044,363 out of 227,498,357
Covered: 49,453,994 out of 227,498,357

Uncovered: 7,109,065 out of 33,980,404
Matches: 18,629,288 out of 33,980,404
Mismatches: 7,534,916 out of 33,980,404
Insertions: 707,135 out of 33,980,404
Identity over aligned base-pairs: 69.3%

Block size distribution

Size range All 184,917 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,566
8.3 kb
10 bp - 100 bp
26,394
1.7 Mb
7,943
561.0 kb
100 bp - 1 kb
140,773
49.6 Mb
39,787
14.1 Mb
1 kb - 10 kb
16,123
25.8 Mb
17,252
42.1 Mb
10 kb - 100 kb
60
1.4 Mb
671
16.7 Mb
100 kb - 1 Mb
1
100.0 kb
30
5.2 Mb