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Solanum lycopersicum vs Olea europaea LastZ results

Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Olea europaea (Olea europaea subsp. europaea, OLEA9) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 105. Solanum lycopersicum 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

ParameterSolanum lycopersicumOlea europaea
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 362,741 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Solanum lycopersicum

Uncovered: 759,784,979 out of 827,747,456
Covered: 67,962,477 out of 827,747,456

Uncovered: 6,925,189 out of 36,416,191
Matches: 20,591,594 out of 36,416,191
Mismatches: 8,258,332 out of 36,416,191
Insertions: 641,076 out of 36,416,191
Identity over aligned base-pairs: 69.8%

Olea europaea

Uncovered: 1,214,142,763 out of 1,315,765,470
Covered: 101,622,707 out of 1,315,765,470

Uncovered: 14,598,696 out of 58,718,063
Matches: 31,281,635 out of 58,718,063
Mismatches: 11,872,578 out of 58,718,063
Insertions: 965,154 out of 58,718,063
Identity over aligned base-pairs: 70.9%

Block size distribution

Size range All 362,741 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,037
15.3 kb
10 bp - 100 bp
65,071
4.4 Mb
31,657
2.3 Mb
100 bp - 1 kb
268,499
89.2 Mb
110,934
38.1 Mb
1 kb - 10 kb
26,073
43.8 Mb
38,181
89.7 Mb
10 kb - 100 kb
61
894.3 kb
571
8.3 Mb