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Medicago truncatula vs Juglans regia LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Juglans regia (Juglans regia, Walnut_2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 104. 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 truncatulaJuglans regia
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 213,750 alignment blocks

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

Uncovered: 357,402,980 out of 412,800,391
Covered: 55,397,411 out of 412,800,391

Uncovered: 16,873,340 out of 50,132,764
Matches: 23,314,565 out of 50,132,764
Mismatches: 9,288,772 out of 50,132,764
Insertions: 656,087 out of 50,132,764
Identity over aligned base-pairs: 70.1%

Juglans regia

Uncovered: 516,061,223 out of 572,786,133
Covered: 56,724,910 out of 572,786,133

Uncovered: 12,457,643 out of 40,412,433
Matches: 19,774,223 out of 40,412,433
Mismatches: 7,471,435 out of 40,412,433
Insertions: 709,132 out of 40,412,433
Identity over aligned base-pairs: 70.7%

Block size distribution

Size range All 213,750 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,259
11.6 kb
10 bp - 100 bp
32,496
2.1 Mb
8,952
649.0 kb
100 bp - 1 kb
163,308
56.0 Mb
48,278
17.3 Mb
1 kb - 10 kb
15,655
24.0 Mb
20,451
48.8 Mb
10 kb - 100 kb
32
955.4 kb
658
13.8 Mb
100 kb - 1 Mb
16
2.6 Mb