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Solanum lycopersicum vs Fraxinus excelsior LastZ results

Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Fraxinus excelsior (Fraxinus excelsior, BATG-0.5) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 109. 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 lycopersicumFraxinus excelsior
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 284,790 alignment blocks

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

Uncovered: 756,811,000 out of 827,747,456
Covered: 70,936,456 out of 827,747,456

Uncovered: 7,402,121 out of 36,416,191
Matches: 20,115,020 out of 36,416,191
Mismatches: 8,295,185 out of 36,416,191
Insertions: 603,865 out of 36,416,191
Identity over aligned base-pairs: 69.3%

Fraxinus excelsior

Uncovered: 787,697,022 out of 867,455,155
Covered: 79,758,133 out of 867,455,155

Uncovered: 9,295,245 out of 45,331,303
Matches: 25,805,561 out of 45,331,303
Mismatches: 9,474,659 out of 45,331,303
Insertions: 755,838 out of 45,331,303
Identity over aligned base-pairs: 71.6%

Block size distribution

Size range All 284,790 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,641
13.4 kb
10 bp - 100 bp
46,367
3.1 Mb
19,282
1.4 Mb
100 bp - 1 kb
214,392
71.6 Mb
84,436
29.4 Mb
1 kb - 10 kb
20,947
36.4 Mb
29,882
72.3 Mb
10 kb - 100 kb
443
7.7 Mb
904
15.7 Mb