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Solanum lycopersicum vs Nicotiana attenuata LastZ results

Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Nicotiana attenuata (Nicotiana attenuata, NIATTr2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. 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 lycopersicumNicotiana attenuata
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 466,411 alignment blocks

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

Uncovered: 682,098,793 out of 827,747,456
Covered: 145,648,663 out of 827,747,456

Uncovered: 6,763,697 out of 35,932,555
Matches: 24,760,184 out of 35,932,555
Mismatches: 4,053,158 out of 35,932,555
Insertions: 355,516 out of 35,932,555
Identity over aligned base-pairs: 84.9%

Nicotiana attenuata

Uncovered: 2,049,846,317 out of 2,365,682,703
Covered: 315,836,386 out of 2,365,682,703

Uncovered: 7,281,589 out of 37,106,589
Matches: 25,215,616 out of 37,106,589
Mismatches: 4,109,732 out of 37,106,589
Insertions: 499,652 out of 37,106,589
Identity over aligned base-pairs: 84.5%

Block size distribution

Size range All 466,411 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
6,379
37.4 kb
10 bp - 100 bp
59,405
3.4 Mb
14,718
992.2 kb
100 bp - 1 kb
289,536
119.8 Mb
66,901
22.2 Mb
1 kb - 10 kb
110,096
226.2 Mb
73,720
249.6 Mb
10 kb - 100 kb
908
28.0 Mb
5,108
99.1 Mb
100 kb - 1 Mb
87
10.6 Mb
120
16.2 Mb