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Medicago truncatula vs Citrullus lanatus LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Citrullus lanatus (Citrullus lanatus, Cla97_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. 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 truncatulaCitrullus lanatus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 164,164 alignment blocks

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

Uncovered: 361,401,493 out of 412,800,391
Covered: 51,398,898 out of 412,800,391

Uncovered: 17,958,496 out of 50,132,764
Matches: 22,012,813 out of 50,132,764
Mismatches: 9,500,597 out of 50,132,764
Insertions: 660,858 out of 50,132,764
Identity over aligned base-pairs: 68.4%

Citrullus lanatus

Uncovered: 327,353,849 out of 365,450,462
Covered: 38,096,613 out of 365,450,462

Uncovered: 4,689,258 out of 26,302,942
Matches: 14,873,961 out of 26,302,942
Mismatches: 6,241,723 out of 26,302,942
Insertions: 498,000 out of 26,302,942
Identity over aligned base-pairs: 68.8%

Block size distribution

Size range All 164,164 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,434
7.4 kb
10 bp - 100 bp
24,438
1.6 Mb
7,653
530.8 kb
100 bp - 1 kb
126,821
43.0 Mb
36,087
13.2 Mb
1 kb - 10 kb
11,405
17.9 Mb
17,741
42.2 Mb
10 kb - 100 kb
66
1.6 Mb
423
7.9 Mb
100 kb - 1 Mb
2
245.0 kb