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Medicago truncatula vs Quercus suber LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Quercus suber (Quercus suber, CorkOak1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 108. 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 truncatulaQuercus suber
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 276,536 alignment blocks

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

Uncovered: 352,149,523 out of 412,800,391
Covered: 60,650,868 out of 412,800,391

Uncovered: 15,005,042 out of 50,132,764
Matches: 24,613,361 out of 50,132,764
Mismatches: 9,763,028 out of 50,132,764
Insertions: 751,333 out of 50,132,764
Identity over aligned base-pairs: 70.1%

Quercus suber

Uncovered: 876,014,643 out of 953,298,670
Covered: 77,284,027 out of 953,298,670

Uncovered: 49,167,232 out of 81,542,507
Matches: 22,648,913 out of 81,542,507
Mismatches: 8,909,284 out of 81,542,507
Insertions: 817,078 out of 81,542,507
Identity over aligned base-pairs: 70.0%

Block size distribution

Size range All 276,536 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,184
11.5 kb
10 bp - 100 bp
39,716
2.6 Mb
15,533
1.1 Mb
100 bp - 1 kb
214,674
72.2 Mb
85,598
29.6 Mb
1 kb - 10 kb
19,892
31.3 Mb
29,542
68.8 Mb
10 kb - 100 kb
70
1.7 Mb
507
8.3 Mb