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Medicago truncatula vs Cucumis melo LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Cucumis melo (Cucumis melo, Melonv4) 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 truncatulaCucumis melo
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 174,133 alignment blocks

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

Uncovered: 362,164,905 out of 412,800,391
Covered: 50,635,486 out of 412,800,391

Uncovered: 17,920,165 out of 50,132,764
Matches: 22,041,706 out of 50,132,764
Mismatches: 9,493,945 out of 50,132,764
Insertions: 676,948 out of 50,132,764
Identity over aligned base-pairs: 68.4%

Cucumis melo

Uncovered: 316,217,504 out of 357,857,370
Covered: 41,639,866 out of 357,857,370

Uncovered: 6,444,355 out of 27,459,425
Matches: 14,409,246 out of 27,459,425
Mismatches: 6,091,194 out of 27,459,425
Insertions: 514,630 out of 27,459,425
Identity over aligned base-pairs: 68.6%

Block size distribution

Size range All 174,133 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,383
7.2 kb
10 bp - 100 bp
25,771
1.7 Mb
8,007
566.1 kb
100 bp - 1 kb
134,721
45.5 Mb
42,181
15.5 Mb
1 kb - 10 kb
12,238
19.4 Mb
18,483
44.0 Mb
10 kb - 100 kb
20
587.6 kb
379
7.1 Mb