In this section

Solanum lycopersicum vs Cynara cardunculus LastZ results

Solanum lycopersicum (Solanum lycopersicum, SL3.0) and Cynara cardunculus (Cynara cardunculus var. scolymus, CcrdV1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 98. 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 lycopersicumCynara cardunculus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 253,742 alignment blocks

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

Uncovered: 769,963,668 out of 827,747,456
Covered: 57,783,788 out of 827,747,456

Uncovered: 8,885,225 out of 36,416,191
Matches: 18,820,110 out of 36,416,191
Mismatches: 8,066,397 out of 36,416,191
Insertions: 644,459 out of 36,416,191
Identity over aligned base-pairs: 68.4%

Cynara cardunculus

Uncovered: 661,715,568 out of 724,667,265
Covered: 62,951,697 out of 724,667,265

Uncovered: 5,996,399 out of 32,068,562
Matches: 17,933,463 out of 32,068,562
Mismatches: 7,572,039 out of 32,068,562
Insertions: 566,661 out of 32,068,562
Identity over aligned base-pairs: 68.8%

Block size distribution

Size range All 253,742 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,009
9.8 kb
10 bp - 100 bp
51,266
3.4 Mb
26,679
1.8 Mb
100 bp - 1 kb
181,743
59.1 Mb
69,877
24.0 Mb
1 kb - 10 kb
18,691
31.2 Mb
27,863
62.6 Mb
10 kb - 100 kb
32
473.4 kb
350
5.8 Mb
100 kb - 1 Mb
1
134.8 kb
1
134.8 kb