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Arabidopsis thaliana vs Solanum lycopersicum LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Solanum lycopersicum (Solanum lycopersicum, SL3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. Arabidopsis thaliana 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

ParameterArabidopsis thalianaSolanum lycopersicum
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 140,482 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 86,133,126 out of 119,667,750
Covered: 33,534,624 out of 119,667,750

Uncovered: 9,617,505 out of 33,775,569
Matches: 16,129,072 out of 33,775,569
Mismatches: 7,480,633 out of 33,775,569
Insertions: 548,359 out of 33,775,569
Identity over aligned base-pairs: 66.8%

Solanum lycopersicum

Uncovered: 789,442,701 out of 827,747,456
Covered: 38,304,755 out of 827,747,456

Uncovered: 11,599,929 out of 35,932,555
Matches: 16,244,367 out of 35,932,555
Mismatches: 7,485,131 out of 35,932,555
Insertions: 603,128 out of 35,932,555
Identity over aligned base-pairs: 66.8%

Block size distribution

Size range All 140,482 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,168
6.2 kb
10 bp - 100 bp
21,528
1.5 Mb
5,433
385.6 kb
100 bp - 1 kb
108,556
36.3 Mb
28,434
11.0 Mb
1 kb - 10 kb
9,227
13.8 Mb
16,274
37.1 Mb
10 kb - 100 kb
3
36.1 kb
202
3.1 Mb